Sunday, August 26, 2012

Invading garlic

Allirai petiolata (garlic mustard)
Garlic mustard is native to Europe, western and central Asia, and nothern Africa. As a biennial, in the first year of growth, plants form clumps of round shaped, slightly wrinkled leaves, that when crushed smell like garlic (hence the name...). The next year plants flower in spring, producing white flowers that release seeds in mid-summer.

Garlic mustard leaves are a great addition to wild salads, providing a mild flavour of both garlic and mustard. Garlic mustard was once used medicinally as a disinfectant or diuretic, and was sometimes used to heal wounds.

In the late 19th century garlic mustard was introduced in North America as a culinary herb, and since has gone on to become a very problematic invasive species. The success of garlic mustard, like that of other invasive species, is due to its lack of native competitors. Garlic mustard produces a variety of compounds that reduces its palatability to herbivores. Interestingly, in its native habitats, some herbivores have co-evolved to feed happily on the plants. But these insects and fungi that feed on it in its native habitats are not present in North America, and this leads to more garlic mustard seeds, allowing it to out-compete native plants. Even white-tailed deer, the scourage of many Eastern woodlands, don't eat the garlic mustard, preferring neighboring plants, which frees even more space for the garlic mustard to spread.

Monday, August 20, 2012

The Harbinger of Summer's End

Sea squill (Drimia maritima)
My favorite plant is easily the sea squill, which in Hebrew is called hatzav (with a hard "h" like your clearing your throat). The sea squill is wondrous because it grows and flowers like a Swiss clock in August in Israel, heralding the end of the summer and the approaching fall. Out of nowhere, the hatzav sprouts and rapidly grows a two-to-three-foot stalk with hundreds of little white flowers. The flowers open over several weeks progressively from the base to the tip, resulting in a very impressive floral display.

How does the hatsav know when August has arrived? It knows this because of the lengthening nights. The sea squill is what's known in scientific terms as a "short day" plant, which is a misnomer, as they are actually "long night" plants. "Short day" plants like sea squill and tobacco flower when the length of the night surpasses a threshold specific for that plant. This is as opposed to "long day" plants like carnations and oats, which flower when the night gets shorter than a set threshold.

Plants "know how long the night is thanks to a group of photoreceptors called phytochromes. In a simple model, phytochromes are activated by red light, and are turned on in the morning; they are deactivated by far-red light, the long waves at the end of sunset, so are turned off as night begins. Plants measure the time the phytochromes are turned off, and use this information to determine season.

Sea squill leaves in winter
Getting back to the seq squill, its floral stalk has no leaves, so where does this plant get energy from photosynthesis? The sea squill has two different life cycles. In the summer and fall, it flowers, but in the winter, when there's pleanty of water for to support photosynthesis and growth it produces large green leaves. Theses leaves produce the sugars that are stored underground in a large bulb. As the dry season starts these leaves wilt and dry up. But the bulb uses these stored sugars as energy to produce the flowering stalk in August.

Wednesday, August 15, 2012

What's an individual?

We expect then that within our bodies, each cell has the same genetic code, the same sequence of DNA, since all of our cells originated from the same fertilized egg. We understand that children are novel genetic combination of their parents, that twins share the same genetic code, and that individuals differ genetically one from the other. Overtime, these genetic differences provide the basis for evolution.

How strange then is the recent report that different parts of the same tree have different DNA sequences!

Ed Yong, reporting from the Ecological Society of America Annual Meeting , tells of the results from the laboratory of Brett Olds, where they determined the DNA sequence from different parts of the same black cottonwood. They found differences in thousands of genes between the topmost bud, the lowermost branch, and the roots.

As Olds told Yong, “This could change the classic paradigm that evolution only happens in a population rather than at an individual level.” 

The differences in the DNA sequences between the branches could conceivably lead to advantageous characteristics. Perhaps different branches of the same tree compete with one another for light, nutrients and pollinators, and this competition leads to Darwinian selection, whereby the most fit branches out-compete their neighboring branches.  The differences in DNA sequence would then be more likely carried on in the next generation by the branches that produced  more or heartier seeds.

Of course the caveat is that this is a blog reporting on a report of a report. i can't wait to see the research article, and for this paradigm to be tested by additional labs using other tree species. If it holds up, we'll have to rewrite some of our textbooks!

Wednesday, August 8, 2012

Peer review - enough with author-blind comments.

I want  to diverge from the normal content of THE DAILY PLANT for a post on a different subject - peer review.

First a disclaimer: I am an Associate Editor of Plant Molecular Biology, and on the Editorial Boards of several other journals, all of which work on the classic model of peer review. I have published over 50 articles following peer review, and got to where I am academically thanks to peer review.

THAT BEING SAID, I too have come to the conclusion that something is majorly wrong with the current state of peer review.

What many people may not be aware of is that not only are reviewers anonymous in giving the author critiques of the manuscript (and rightly so perhaps), they can ding a manuscript by comments to the editor that the author never sees!

Case in point, I got the following email recently:
Your manuscript entitled "Biochemical and Biophysical Studies of (bla bla)" was reviewed by the Editorial Board. Unfortunately, the manuscript was found to be unacceptable for publication in the Journal of Good but not Top Science in its current form. The reviewers felt the work is of interest. There were some specific concerns with the manuscript, however, including the lack of specific data elements and the absence of functional supporting data. The deficiencies noted by the reviewers are sufficient to preclude acceptance of the manuscript. However, we encourage you to address the concerns, provide additional data, and submit a revised manuscript to the Journal. 

Both reviewers basically asked for the same things about five changes in the figures, all concerned with presentation of controls. All valid critiques.

So why was the manuscript rejected? Because of, according to the Editor's letter, "the absence of functional supporting data". But none of the reviews supplied to us asked for this! We therfore wrote the editor the following query:
It would be most helpful if you could clarify a clause in your email over which we are puzzling. You wrote "There were some specific concerns with the manuscript, however, including the lack of specific data elements and the absence of functional supporting data." From the reviewers' comments, we can easily identify the "lack of specific data elements" which we will rectify. However, their comments do not indicate or specify what you meant by "the absence of functional supporting data" in your decision summary. We would be most grateful if you could provide some further explanation so that we do not prepare a revision lacking the requested material, resulting in frustration by all parties. 

The Editor's response:
I will consult with the reviewer who used the term "absence of functional supported data" so that we can clarify exactly what was meant. I will get back to you after that. 
In other words, the Editor had no idea why he was rejecting the manuscript, likely had not read the entire manuscript, and was apparently basing his decision on an author-blinded general comment to the Editor!

What is the role of anonymous peer review if a reviewer can use top-secret comments to the Editor to kill a manuscript, without ever having to justify this to the authors? If the reviewer (and we don't know if it was #1 or #2) had criticisms of our science, we have the right to read them - that's what review is, and we also have the right to argue a rebuttal. But author-blind comments are just another form of reviewer tyranny, giving anonymous reviewers undue licence to critique without being held responsible by the author. I call on all journals, including the ones I'm involved with, to cancel the option of author-blind comments so that authors can at least be presented with all the criticism of their work.

The postcript of this is, that it took the Editor two weeks to get an answer for us as to what "functional supported data" is, at least what it is according to the reviewer. Now presented with the critique, we can decide which experiments to do, rebutt the critique, or send the manuscript elsewhere. (We've opted for a mixture of options 1 and 2).

And I feel better having ventilated!