The Peer-Review Process: Problems and Pitfalls, but it's Worth Saving!

The peer-review process for research articles is a well-established method of screening new results prior to being released to a larger audience. The results of peer-review are supposed to mean that if you read information in a peer-reviewed journal, you can be assured that what is being said makes sense and the information can be used as a sound basis for making decisions.

I should note at this point that I have reviewed articles for many international journals and am an Associate Editor for the American Journal of Enology and Viticulture. In that capacity I screen manuscripts for suitability (e.g. is it within the scope of the Journal, are there glaring errors in science etc.) before sending it out to two people with relevant experience for critical review. I take those reviewer comments, see if they are fair, and then pass them back to the authors for them to consider in revising the document. That is then submitted again and I would look to see if they have addressed all the relevant reviewer comments. If so, the paper is accepted for publication. If not, it may go back for further review, or rejected.

It's not a perfect system (it can take a long time to go through this process, you have potential biases from reviewers, it tends to be a conservative process etc.), but if you look after it well it does a good job.

All researchers that submit manuscripts for peer-review should be giving back to that process by accepting manuscripts to review for those journals -although there are a lot of questions about that process, too, as the people who do the reviewing work provide the engine that runs many for-profit publishers...

However, that aside, the model of peer-review is under fairly extreme pressure. The basis of the process is that people who have expertise in an area of research will do a critical review of papers submitted for publication. The key words there are "critical review."

In my experience, it takes some time to do this. Even screening an article before sending it out to reviewers can take more than an hour, and for me to do a proper review (which includes reading it carefully, researching problematic statements, and then typing up comments) takes about four hours or more.

Researchers have less and less time available to them for a variety of reasons - with constant reductions in budgets, we have more administrative duties. With non-replacement of staff, we're taking on more teaching. There is increased pressure to find external research dollars. There is increased pressure to publish, leading to taking on more research students. In short, we have less and less time to devote to something that produces no tangible benefit to our employers. Four hours spent doing a quality review of a manuscript is four hours spent not doing all the things that a employers wants.

So as an Associate Editor, I'm finding some reviews quite superficial. Increasingly, I also find it difficult to get someone to agree to doing a review in the first place.

As a reviewer, I still try to spend all the time that's necessary to do quality work, but this does come at a cost, personally and professionally.

This latest news item, "Major publisher retracts 43 scientific papers amid wider fake peer-review scandal," is not an isolated example. A visit to Retraction Watch will easily demonstrate this, though some papers are retracted for honest reasons.

But the article mentioned does highlight the problem with peer-review: It was developed in an era when researchers had more time - research money was not as highly contested, teaching loads were less, there was no pressure to publish - you published when you though the data were ready etc. There was plenty of time to pore over someone else's manuscript and give a thoughtful review of its content.

Some of the issues identified in the article linked above should have been caught by the associate editors of the journal -they are supposed to be choosing reviewers for the papers carefully before the paper is sent out: looking for connections between authors and reviewers, checking on the backgrounds of  reviewers and the like. The fact that they have not been doing this is another indication that people working with the papers are under pressure and feel they can't afford to take the time to look over the situation carefully.

So is peer-review doomed? I certainly hope not. The process has much merit to it, but it will struggle to survive until employers recognise the importance of peer-review to science progress. There needs to be a system in place where review of manuscripts is thought of as being of some importance - not as much as publishing a paper, but it needs to give some kudos to those who do it, and especially those who do it well.

Herbicide damage when converting to organics?

UPDATE: (June 2014)
More investigations by the vineyard manager all seem to point to the seaweed spray being associated with the symptoms. The explanation below (that the phosphate in the spray is causing the release of bound glyphosate) is still a possibility, but it is also possible that plant growth regulator-like substances in the seaweed spray are interacting with other environmental factors to cause the shoot tissues to respond, and glyphosate residue is not involved.

However, the exact cause is still a mystery!


Original post:
I recently visited a vineyard where vines were exhibiting classic glyphosate damage symptoms. Not so unusual, you say, except that this wasn't in patches - it was pretty even over the whole vineyard, spanning vines of different ages, rootstocks and varieties... Drift from another property was ruled out as surrounding vineyards were fine...

The vineyard had only recently converted to organics from years as a conventionally managed weed-free strip under the vines, created by the use of glyphosate (e.g. Roundup).

Symptoms appeared towards the end of November, after cultivation under the vines had been done. This is not the first time this sort of thing has happened (organics guru Bart Arnst has observed this sort of thing before). Could there be a link between the symptoms and the cultivation? Conventional thought is that glyphosate is rapidly inactivated when it comes into contact with the soil, so how could this be possible?

Well, that last statement is usually misinterpreted. Yes, it's inactivated, but that's not the same as being degraded and rendered harmless...

A bit of research shows that glyphosate is stable in sunlight, and tightly bound to soil particles (Rueppel et al., 1977), particularly clays and particularly in those that have high levels of aluminium and iron. Soil pH is also important, with higher adsorption rates at lower pH values (see Borggaard and Gimsing (2008) for a review on the topic). 

Soil organic matter has variable effects on glyphosate adsorption, but generally results in no change or tends to decrease it due to its blocking of binding sites in the soil (Gerritse et al., 1996), though studies exist to say the contrary (e.g. Sprankle et al., 1975).

Glyphosate can be degraded by soil micro-organisms, but generally not when it is bound to soil particles. The ability of a soil to mineralise the herbicide seems to correlate pretty well with general soil microbial activity, but few species have been identified that can directly act on the molecule itself (Borggaard and Gimsing, 2008; Forlani et al.,1999).  Because of all these variables, the half life of glyphosate in the soil varies from days to months.

The upshot of all this is that the glyphosate sprayed on the soil doesn't disappear - it is bound to soil particles and can be degraded only under the right conditions. Those conditions include levels of microbial activity, but surprise surprise, there isn't a lot of that near the surface of a herbicide-treated soil (Reinecke et al., 2008; Whitelaw-Weckert et al., 2009). Microbes need moisture, nutrients and organic matter to do well, and none of those are very common near the surface of a herbicide strip.

So this is evidence that glyphosate applied season after season is still present in the vineyard, but why does it become a problem when cultivation starts?

A little more digging (pardon the pun...) reveals that glyphosate and phosphate compete for binding sites in the soil, so adding phosphate to soil could release glyphosate (Gimsing and Borggaard,2001). This is why high phosphate soils can bind less glyphosate in the first place (Sprankle et al., 1975).

So here is a possible explanation! The vines in this case had a soil drench of seaweed extract and fish oil, which could have relatively high levels of phosphates. These could have encouraged glyphosate to de-sorb from the clay particles and be taken up by the roots.

Even then, I suspect there is an interaction with rainfall events as the symptoms appeared to stop developing, but later came back after a significant rain event. It's possible that there is renewed root growth into the herbicide-containing soil, leading to more uptake.

Curiously, reports are that the shoots arising from the base of the vine trunks show no symptoms.

As with every other season, there is at least one situation that makes you scratch your head and go, "Huh???"

If anyone has similar experiences, please leave a comment!!

 

Climate change and its interaction with winegrowing

A Radio NZ article about University of Waikato student Electra Kalaugher and her work on climate change and dairy farms, and the accompanying video was particularly timely, because at about the same time I was answering a questionnaire sent to me by a student studying an MBA in Bordeaux. Her thesis is on climate change on winemaking and how it concerns the French legislation relating to the wine industry.

Below are her questions and my answers to them. My thanks to her for permission to post the information here...

1-Climate change has been affecting the wine industry, like all fields in agriculture. What is your experience in the vineyards of New Zealand so far?

Of those events that are supposed to be altered with climate change, in recent years I think we have seen wider swings in weather events, such as rainfall, snow, frosts and the like. We have had some periods of significant drought, as well as highly unusual heavy rainfall. We have seen some late season frosts, and unusually large amounts of snow in some areas. However, it remains to be seen whether these events are considered to be abnormal in the longer term.

2-Do you think New Zealand will benefit from the climate change since the warmer areas expand?

It is possible that new geographic areas will open up to winegrowing as a result of the overall warmer temperatures. However, this will have implications for the existing areas, where the warmer climate may mean that making wine styles associated with a particular region could be made more difficult. For example, the Marlborough style of Sauvignon blanc is associated with the cooler ripening period that the region has experience. If temperatures rise, the flavours in the wines will also change, and so the wine style.

This is one challenge, and another significant one is the chance of more extreme weather events. Of the possibilities, early season or late season frosts are a particular concern for the wine industry, as many areas are already prone to damaging frost events, so having them occur later into the growing season, and earlier as the season ends and harvest approaches, will have a direct impact on profitability.

Some forecasts for seasonal changes in precipitation point to less overall rainfall as a result of climate change in the eastern parts of New Zealand. Therefore, water will become an even more valuable resource, potentially limiting grape production.

Overall, I do not think that climate change will be a beneficial thing for the New Zealand wine industry, but the reality is that we will have to deal with it.

3-What are the challenges that the wine producers have been facing due to climate change effects?

I've mentioned some of these already - the possibility of frosts happening later in the beginning of the season and also happening before fruit is harvested. Water availability has been an issue with the establishment of newer vineyards, with water schemes needing to be developed to ensure a reasonably reliable water supply. Increased heat means that some grapevines will need to be grown slightly differently in order to retain the flavour profiles that are wanted in the wine. Severe flooding has had minor impacts on vines so far, but this will probably be more of an issue in the future.

4-What kind of changes should be made in the vineyards in order to adapt the shift in climate?

Viticulturally, it will be necessary to change the management of the vines to retain flavour profiles - for example, doing less leaf removal, or changing its timing. Trellising systems may need to be changed to help with this, as Vertical Shoot Positioning, which is the most widely used system in New Zealand, may give the fruit too much exposure.

Irrigation management (and linked with that, cover crop management) will have to be tweaked to ensure vines don't get water stressed at inappropriate times. More efficient ways of delivering water to the vines, and measuring soil and grapevine water status, need to be developed.

With frost events potentially happening when vines have more canopy on them, more efficient ways of dealing with frosts will be needed. If enough water can be found (which is unlikely for large vineyards), sprinkler systems will work, but most are using fans or helicopters at the moment, which rely on the presence of an inversion layer, which holds warm air. As well, it isn't certain how climate change will alter the occurrence and strength of inversion layers...

New vineyards should be planted with future shifts in climate in mind. This encompasses most aspects of vineyards, but also variety choice and potential wine styles to be produced.

5-As a viticulturist, what are your conclusions for the future concerning the climate change effects, for New Zealand and also globally?

In my mind at least, climate change is a reality that we should be ready for. Planning for its occurrence, using the latest forecasts (e.g. NIWA's Climate Change Scenarios for New Zealand), is the best we can do. 

The wine industry will be able to cope with climate change, but it will likely have an impact on the financial planning, with increased risk of crop loss and increased management costs. The possible changes to wine style also need to be considered carefully, as the consumer may want to stick with the current style, but it may not be able to be grown in the same area or it wouldn't be cost effective to do so given the extra labour inputs.

What's the weather doing this season?

The Growing Degree Days (GDD) figures for Lincoln through March 13th don't make for pretty reading!!

Currently we sit at 686 GDD (base 10, calculated on a daily basis) while the long term average (LTA, 1931 through 2010) to this point in the season is 812.

 Figure showing the growing degree days for Lincoln, Canterbury based on daily calculations at base 10C

December was the only decent month, having a heat accumulation close to that of LTA, but November, January and February were all cooler than LTA to the tune of about 85% of the value.

Rainfall is about aligned with LTA, the current season to March 13 being about 18mm greater than the LTA of 441mm.

Often, we get a nice March and early April after seasons where the early months' temperatures have been lower than average, but so far this doesn't look like it's happening, with the weather patterns seemingly stuck on cool and unsettled.

The Seasonal Forecast for New Zealand (http://www.niwa.co.nz/seasonal-climate-outlook-march-may-2012) indicates they are expecting more winds from the north-east, which for many of the growing regions in New Zealand, which are along the East coast of the country, means cooler temperatures.

When I look back at the pattern of heat accumulation for Lincoln Uni since the 1998-1999 season when I first arrived in Canterbury, this is the coolest season of them all, bar the 2000-2001 vintage. It's also been a remarkably consistently cool season, whereas in other years it tends to be warmer than LTA at first, then cooler nearer to harvest or vice versa.

So what does this mean for vintage? As long as the fruit stays free of disease (which we've been encouraging through an open canopy), we should be all right. Any opportunity to drop off crop that is tailing behind the average in terms of ripening is a good idea, as well as keeping the canopy open so the fruit dries out more quickly and also gets warming by the sun. We also have to hope that the night-time temperatures don't get too low, as this can be a signal for the vines to get ready for winter and start dropping their leaves! We've already had a couple of nights near 3C!

Our own vineyard, in which we're growing Pinot noir (and a bit of Pinot meunier) for sparkling wine is about 10km from the Lincoln Uni vineyard, but we're harvesting very shortly as the fruit is up to 19 Brix. In a season like this, this show the value of site selection (our vineyard is on the Port Hills and protected from the easterly (and cool) winds), good canopy management and end use of the grapes (sparkling wine, so they are harvested earlier). Of course, that isn't saying anything about how easy it is to sell the wine!

I suppose the good news out of all of this bad weather information is that the December temperatures were reasonably warm, which should mean we still have a decent initiation of flower clusters for the 2012-2013 vintage. 

At least we will have a promising potential to work with!!

Selecting the Right Clusters for Your Wine

This article will appear in the Wines of Canterbury Newsletter

"Quality is never an accident" - usually attributed to William Foster or John Ruskin

Colour change and ripening has begun in our grapes, and a lot of people start thinking about cluster thinning at this time. But have you stopped to think about why you're doing this? Here are some possible answers and few thoughts on each:

• To reduce the crop load

Yes, true. But it takes time and money to do this, and at the same time, you're reducing the amount of fruit harvested and paid for. There has to be more to it than this!

• To make the winemaker happy

At the recent International Cool Climate Symposium for Viticulture and Oenology in Tasmania, Richard Smart said the best time to start thinning your crop was just before the winemaker visited the vineyard, and the best time to stop was as soon as he left!

The best way to make the winemaker happy is to deliver high quality fruit in relation to what they are paying. Do all winemakers know enough about viticulture and the production of high quality grapes to be able to tell you what is and isn't right for the vines? Some do, but many don't. Their heads should be filled with all things winemaking, and viticulturists' should be filled with all things viticultural.

The best thing to do is get the winemaker to tell you what s/he wants from the vineyard's fruit, and for you to do what's necessary to have fruit that most closely meets those needs. Sometimes, removing lots of fruit is not the answer!

• To increase sugar accumulation in the fruit

If you go through a vineyard at veraison and remove fruit randomly, I doubt there would be much, if any difference in the harvested fruit composition - that is, the rate of sugar accumulation in the remaining fruit is no faster because you've removed some crop. I haven't seen any consistent and convincing evidence to suggest that removing crop randomly this late in the season brings harvest forward.

However, if we do commercial practice and remove that fruit which is not as ripe as the rest (in the left side of the figure below), then we're decreasing the variability of that fruit by removing the less ripe stuff, and thereby increasing the average ripeness of what remains. So what's happening there is removal the tail end of ripening fruit.

By doing this, you can increase the quality of the resulting wine, which is the overall goal of the viticulture-wine making pathway that we all travel along, and therefore the goal of crop thinning.

Because fruit are being removed selectively, and there will always be some fruit that lags behind in development, this form of thinning can be effective in improving wine quality in any season - particularly in cooler climates, where getting fruit to its optimum ripeness is a challenge.

But it doesn't stop there. If we want to maximise the quality of the wine made from the grapes, we need to ensure that only the best quality fruit ends up in the receival bin at the winery. This process continues on from crop thinning to monitoring the fruit and fixing problems before they arrive, so you have the greatest amount of harvestable crop possible. Things to think about here are:

• Removing leaves resting directly on clusters. Airflow around and if possible, through, clusters is a very important part of keeping Botrytis at bay! Leaves on top of, or resting next to, clusters keeps the environment more humid and for longer, which is what Botrytis needs to germinate and infect.
• Similarly, arranging clusters so they are not draped on top of one another. Multiple clusters trying to occupy the same space mean restricted airflow and poor exposure to the sun, leading to greater disease risk and less ripe flavours. The best time to combat this is even a few weeks after fruit set, when it's easier to separate clusters and try to arrange them so they don't touch. If you can't keep them from sitting on top of one another, take the short term loss by clipping off of one of the clusters rather than doing nothing and having the real risk of losing all the fruit to rot.
• Cutting out clusters or parts of clusters damaged or diseased. Physically damaged fruit can, and usually does, harbour Botrytis - something most evident when a couple of weeks ago I took a few split berries i found in the vineyard (like those pictured below)  and incubated them in high humidity conditions for a day or two. Lots of fungal growth appeared from the damaged areas, but none from the intact parts of the berry. As well, fruit that has a bit of Powdery Mildew on it can split when the berry starts to ripen, inviting Botrytis and other rot organisms. Once it's in and established, it's much more likely to spread around.
  
  
  
  
  
• If you're machine harvesting, have a crew go through beforehand to remove any second set crop that might also be harvested, because even a small amount in a load can have a significant effect on wine flavour. As well, have them take out any diseased or sunburnt fruit, as these can lower the quality of the wine. Monitor their work for slips and keep them on the right track.
• If you're hand harvesting, the best time to sort grapes is in the vineyard, not on a winery sorting table. Why pick and transport poor quality and diseased fruit, only to discard it at the winery? You make more work for yourself, and increase the risk of spreading the disease around. Make sure your picking crew is well trained to leave the undesirable fruit, and check on them periodically to make sure they continue to do it right.

While this is all sound advice, I'm not trying to say that it's right for everyone. For some wine products, this level of attention to detail is not warranted - there just isn't the payback to justify it. However, if you're thinking about quality first, then every little bit counts. There isn't one, single, management decision that will deliver quality to the winery - it's a series of actions that contribute to the health and suitability of the harvested crop that makes the difference...

Can we "grow" wine?

This issue has come up a few times in my circles recently.

We have used in various documents the word "winegrowing" or the phrase "winegrowing industry" to describe the grape and wine industry. More than a few people have come back and said that no such word exists because cannot grow wine, and suggested alternatives such as grape growing, wine producing etc.

I did a bit of searching to see how commonly used it is - I already knew it was well-used in New Zealand, as the national grape grower and wine maker organisation is called New Zealand Winegrowers (http://www.nzwine.com/) and their national publication is called the New Zealand Winegrower magazine (http://www.ruralnewsgroup.co.nz/winegrower).

Most of the regional grape grower and wine maker organisations include "winegrowing" in their name New Zealand Winegrowers and is used in the popular press, e.g. in New Zealand, and article in Stuff.co.nz and it's associated publication the Marlborough Express, as well as the New Zealand Herald.

Overseas it's used in the popular press, too: The Wine News, Australian Broadcasting Corporation, The Independent....

As well, there are several organisations overseas that incorporate the word into their names:

The California Sustainable Winegrowing Program

The Valais Museum of Wine and Winegrowing

The wine company Krauthaker in Croatia

And in the Texas Wine Regions web site

(did you know that Texas ranks Fifth in wine production in the USA?)

Surprisingly to me, it is also not a new term, being used in the popular press back in the 1960s and 70s

An of course, there's even a Facebook page about it:

So a bit of research finds that yes, it is a common term and that it isn't a new one (at least, in the English Language - I haven't checked for translations of foreign words that might mean the same thing).

This all makes sense, as in essence, we do grow wine. Wine quality comes about to a very large extent from where and how the vines are grown, as this affects the composition of the grapes and the wine that is made from them.

Winegrowing as a term has come about, in my opinion, from the recognition of the importance of the grape, and how it is cultured, to wine production. The essence of wine comes from where the grapes were grown and the manner in which the vines were managed.

And this is what keeps most wine from being a commodity!

Shoot thinning - The importance of keeping your head clear

Note -this post is based on an article I wrote for the Wines of Canterbury newsletter this month...

Spring is all around us in Canterbury, and the grapevines have responded by shooting away madly. From trying to keep pace with the grass growth (trying to keep it as short as possible), now that the frost season is (hopefully) dying away, my attentions have turned to canopy management.

On the ideal, balanced, vine we get even bud break and shoot development and one shoot arising per node left at pruning. While we all strive for the ideal vine, it is something that rarely occurs, so we are left dealing with reality - in the case of my five year old Pinot noir vines, reality means that I occasionally get more than one shoot per node left, and there are a considerable number of extra (non-count) shoots coming from the head region.

Because I have only a backpack airblast sprayer for my own vineyard, the air turbulence it makes isn't all that good, and therefore neither is spray coverage. I need an open canopy to make the most of what the blower can deliver. So this means I can't tolerate all the extra, non-count shoots that have popped up on the vines.

The ideal shoot density for a VSP-type system is around 15 shoots per metre of row, or about 6-7cm between shoots. On cane pruned vines, the internode length of the cane laid down during pruning determined the spacing of the nodes and therefore the expected shoots in spring. So if you have used canes with a shorter internode than this, you will have a potential problem. For me, 18 shoots per metre of row (about 5.5cm between shoots) is okay, but every time you increase the number of shoots per length of row, you're increasing the risk of poor fruit exposure and lesser air movement - neither of which is desirable. And this is not even considering the possibility of extra shoots coming up from nodes or from the older wood around the head.

So I went through a did shoot thinning the last couple of weekends. The general rule is, retain only one shoot per node left at pruning, and if you're taking one off, remove the one with less crop. However, there are times when I left the second shoot on. This happened when there was a blind node next to the node with two shoots - in that case, I would often leave the two shoots, so as to make sure the canopy was continuous and to keep the average shoot number per metre near its target.

Other times, the internodes were shorter than ideal on the cane that I laid down, so then I might remove a shoot from a node position to make way for the neighbouring shoots (see Figure 1).

Figure 1. Compressed internode leading to two closely spaced shoots. I took off the ones (there is a secondary, non-count, shoot pointing toward the camera) on the centre-right to open things up a bit

 

 

 

In yet other cases, shoots would be growing out from the lower side of a cane and shooting sideways rather than up (see Figure 2). I will remove these, too, if they are going to grow to the side and therefore put a lot of leaf in the fruiting zone.

Figure 2. A sneaky sideways slithering shoot. Definitely up to no good!!

Around the head of the vine things get a bit trickier. A mantra of mine is that thoughts about pruning carry on through the rest of the season. If there is a non-count shoot that could be of use when it comes to pruning later in 2012, then I take pains to preserve it! For instance, I have a couple of vines where the canes laid down originate very close to the fruiting wire, but no growth is available below it to leave as a spur. Therefore, if I get any kind of growth below the wire, I hope to save that in the hope that it might become a decent spur to leave at pruning, or better yet, leave as a cane.

This means I take a bit of extra time to ensure I don't remove something potentially important, but then when it comes to pruning next year, it will make the job easier and therefore faster.

The before and after pictures of shoot thinning can be quite enlightening (Figure 3)! There should be quite a bit of space between shoots at this time of year, which is good for the development of flower clusters for the 2013 vintage (they will be initiated in the month of December, so good light exposure now should mean good light exposure until flowering) and good for airflow.

Figure 3. Before and after pictures of shoot thinning around the head region on a 12 year old Pinot noir vine. Note that no shoots have been left at the top of the head - this is because it's very close to the fruiting wire, so shoots arising from there wouldn't be able to be used effectively at pruning. As well, opening up the head area leaves space for the shoots coming up from below the wire.

The reason why I do this thinning now is that it's a lot easier to see all the shoots, and a lot easier to take them off (especially without damaging neighbouring shoots), but also because I want to ensure I get good spray coverage - some areas around the heads are very densely packed with shoots.

On my ultra-premium vineyard, labour is something that I try not to skimp on. After all, when an academic plants a vineyard, it's bound to be under a lot of scrutiny!!