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September 26, 2012

Diversity of Opinions on Diversity

Cedar Creek plots weeded to maintain low diversity have low plant cover, explaining their low productivity. But why does that space stay open?

Part two of the mostly positive review by Jeremy Cherfas, on the Agricultural Biodiversity blog, argues that my Darwinian Agriculture book understates the benefits of mixing varieties (e.g., with different disease-resistance genes) within a field.

I added a comment there, noting that I had included a comparison of this strategy to an alternative way of deploying the same amount of genetic diversity. But his overall point remains valid. I think I over-reacted to what I see as a tendency to think about crop diversity mainly at fine spatial scales, while ignoring diversity at larger spatial scales and over time.

While I'm on the subject of plant diversity, I talked to Dave Tilman about the suggestion in the book that the low plant cover (see above) in his low-diversity treatments could be an artifact from their weeding protocol. He apparently has data showing that seedlings of the one "resident" species in his monoculture plots do poorly, relative to seedlings of other species. I've seen the same mechanism as an explanation for high tree-species diversity in the tropics -- species X doesn't do well near species X, perhaps due to disease.

The fact remains, however, that photons hitting soil, rather than leaves, drive water loss without contributing to photosynthesis. So it's not surprising that low-cover plots have low productivity. Crop monocultures, however, usually achieve full cover, limiting the relevance of this work to agriculture.

If I get to do a second edition, I will try to correct these flaws. Meanwhile, I see thoughtful negative comments as positive, consistent with my goal of stimulating more-insightful discussion.

Two science scams in one day !

I've written about fake scientific conferences, but here's the latest twist on vanity publishing for scientists. A company called Research Media has offered to write about our research in a "special journal" called International Innovation, in exchange for $2930. Needless to say, our library doesn't carry this "journal."

Also, someone offered to write a favorable review of my book on Amazon in exchange for endorsing her Kickstarter project. She wasn't quite that explicit, of course.

Do people really think scientists are stupid?

September 25, 2012

Blogs discussing Darwinian Agriculture

The bloggers and commentators at Agricultural Biodiversity set the standard for insightful discussion of many agricultural issues, so I was hoping they would review my book. Jeremy Cherfas has just posted the first half of a two-part review.

Tyler Cowen also mentions my book, briefly, in the web version of his op-ed on world hunger in the New York Times, posted on his blog, Marginal Revolution.

Cherfas's review and Cowen's mention are both positive. Both are reasonable summaries. Both somewhat over-state my doubts about biotechnology's potential, however. Yes, many of the approaches suggested or tried by biotechnologists have already been tested and rejected by natural selection. But some tradeoffs rejected by natural selection may be acceptable to us. Less-bitter cucumbers may attract rabbits, but we can build fences.

Eventually, we may learn how to design and implement improvements so radically different from anything that exists now that they have never been tested by natural selection. Radical innovations may carry unknown risks, however.

September 24, 2012

Comments on Forbes article on biomimicry

Steven Kotler, at Forbes, recently posted a story titled "Move Over Genetic-Engineering; Biomimicry Seems The Better Bet For Solving Global Hunger."

The Forbes site said I could comment using my Google identity, if they could just have access to my contact list. No thanks. I"m amazed it's even legal to ask, if it is.

So I'll comment here. Biomimicry is a major theme of my recently published book, Darwinian Agriculture -- but biomimicry of what?

The adaptations of individual plants, animals, and microbes have been improved (by the criterion of Darwinian fitness in past environments) through millions of years of competitive testing against alternatives. But larger-scale patterns we see in nature, such as the total number of species in a forest, or how trees are arranged, haven't been tested competitively. Trees compete against trees, but forests don't compete against forests.

If we copy individual adaptations of trees, we are copying the winners of many past rounds of competition. A forest may have persisted for thousands of years, so it's probably not too dysfunctional. But it hasn't been tested through repeated competition, so there's likely to be plenty of room for improvement.

I would have expected a writer at Forbes -- do they still call themselves "a capitalist tool?" -- to understand how competition is key to improvement, but apparently not.

Now, what about the specific examples in the Forbes post? Spiders compete against spiders and sharks compete against sharks, so it's not surprising that spider silk and shark skin are awesome.

But his "favorite" example is that wildlife corridors that mimic electric circuits work better. I'm not sure what point Kotler is trying to make here -- did he not notice that this is biomimicry in the opposite direction? Although caribou have competed against caribou, curved and straight wildlife migration corridors haven't competed against each other. (OK, maybe they have competed for caribou and their manure, sort of, but the winning corridors don't produce "offspring" with the same degree of curvature.) So this case calls for intelligent design by humans, not mimicry of large-scale patterns seen in nature.

And then there's the endophyte example. Some fungi that live inside plants can provide major benefits to those plants. We will be reading and discussing journal articles about this in a couple weeks, in our graduate seminar.

If there were only one fungus per plant, fungi that benefit their hosts would thereby benefit themselves. But mixed infections seems to be common. With mixed infection, a fungus that invests resources to benefit the host is like someone who pays taxes when nobody else does. Admirable, perhaps, but not likely to be very successful. It's a variation on the classic "tragedy of the commons."

One benefit often provided by endophytes is chemical defense against a plant's enemies. This case isn't too hard to understand. Maybe the various fungi make toxic chemicals to attack each other, since they're competing for the same plant resources, and those same toxins also protect against insects that might otherwise eat the plant.

But how and why do endophytes improve drought tolerance? Unlike mycorrhizal fungi, which extend out into the soil, most endophytes are entirely inside the plant. So it's not as if they can pull more water out of the soil. Sure, they can produce chemicals that mimic plant hormones, thereby manipulating the plant to make more (or fewer) roots or to open (or close) the stomata through which water evaporates from leaves.

But it's hard for me to believe that:
1) a fungus infecting a plant is a better judge of how many roots a plant needs than the plant is
2) that the fungus would put the plant's interests ahead of its own.

It's a mystery. But that's what science does: solve mysteries. Stay tuned.

September 14, 2012

This week: fossils, epidemics, cooperation, and aging

Arthropods in amber from the Triassic Period "arthropods some 100 Ma older than the earliest prior records in amber"

Unifying the spatial epidemiology and molecular evolution of emerging epidemics "spatial parameters of an emerging epidemic [can] be directly estimated from sampled pathogen genome sequences"

Evolution of cooperation and skew under imperfect information "full cooperation may not be achievable due to private information over individuals' outside options"

No third-party punishment in chimpanzees "Dominants retaliated when their own food was stolen, but they did not punish when the food of third-parties was stolen, even when the victim was related to them. "

Ageing: Mixed results for dieting monkeys
Impact of caloric restriction on health and survival in rhesus monkeys from the NIA study "Our study suggests a separation between health effects, morbidity and mortality"

September 12, 2012

Ink content of inkjet cartridges

I saw a discussion where everyone was complaining that "pages per cartridge" is a meaningless number. They wanted to know the actual ink content per cartridge to compare different options. OK, here's a start:

New CC643W cartridge weighs 35.8 grams
Used CC643W cartridge weighs 29.8 grams
So there's 6 grams of ink per CC643W cartridge (from HP).

Canon 3e black 53.1-21.4 = 31.7 gram ink per cartridge.

If you have similar data for other options, add them as a comment. Comments without actual data (promotional "fluff") will be deleted.

September 11, 2012

Somebody liked my book

The first customer review on Amazon.uk is positive, aside from the statement that the book is "at times a bit repetitive." I have to agree. I thought repeating some key points would help those who just read particular sections, but I may have overdone it.

Amazon's US branch doesn't have any customer reviews yet, just reviews from two experts contacted by the publisher.

September 7, 2012

This week's picks

Stone tool production and utilization by bonobo-chimpanzees (Pan paniscus)
Just last week, we gave a kid a copy of "Monkey with a tool belt." No, this paper doesn't show that humans are descended from bonobos. DNA evidence shows that the bonobo-chimp split occurred after humans split from the common ancestor of all three.

Reproductive queue without overt conflict in the primitively eusocial wasp Ropalidia marginata "The dominance rank of an individual is not a significant predictor of its position in the succession hierarchy. "

Predatory Fish Select for Coordinated Collective Motion in Virtual Prey
"collective motion could evolve as a response to predation, without prey being able to detect and respond to predators"

Profibrogenic chemokines and viral evolution predict rapid progression of hepatitis C to cirrhosis
"disease severity is predicted by the evolutionary dynamics of hepatitis C virus"

September 5, 2012

Biomimicry of forests or trees?

A colleague is teaching a class on biomimicry and asked whether I had a short summary of evolution as background. I gave him part of "Evolution 101", Chapter 3 of my book on Darwinian Agriculture, but also some material the editor made me leave out. Here it is:

A brief analogy with engineering may be useful. Imagine that a pair of ideas-from-nature experts were asked to help engineers improve a bicycle safety helmet. Ideally, they would like to increase fracture resistance, while decreasing weight. Here's how the discussion might go.

Ideas-from-nature expert #1: "Consider mimicking the structure of conch shells. I don't know anything about their structure, but I do know that sting rays have been eating conchs for millions of years, by crushing their shells. Whichever conchs had the toughest shells were most likely to survive and reproduce, all else being equal, because the rays would give up on them and go crack a weaker conch. Whenever mutations arose that made shells stronger, those mutants would have tended to survive longer, so their descendants have displaced those who made slightly weaker shells. This process has been repeated for millions of years, so the structure of conch shells is probably pretty good by now."

Engineer (one week later): "We tested conch shells and their fracture-resistance is indeed amazing (Kamat,S. 2000). Microscopy reveals that conch shells have alternate layers of hard minerals and stretchy organic material. We have some man-made materials with similar properties, but I think we can improve on the conch-shell design. In particular, we could make each of the two kinds of layers thicker. Thicker layers will probably make the material even stronger."

Ideas-from-nature expert #1: "Maybe, but surely mutant conchs with thicker layers must have arisen repeatedly. If thicker layers are better, why didn't conchs with thicker layers in their shells displace conchs with thinner layers?"

Engineer: "Interesting question. Maybe thinner layers actually give better interaction between the two materials. Also, thicker layers would be heavier, for a given number of layers."

Ideas-from-nature expert #1: "And a conch with a heavier shell couldn't swim as fast. Natural selection balanced the tradeoff between strength and weight. Evolution is all about such tradeoffs. We can't be sure that conchs have evolved the best possible compromise between shell strength and weight, but it's probably better than most slightly different alternatives. That's because alternatives that are only slightly different have probably arisen via mutation, and tested through indirect, sting-ray-imposed competition."

Engineer: "OK, but our bike helmets will also be exposed to ultraviolet light from the sun. Conch shells didn't have that additional challenge."

Ideas-from-nature expert #1: "Right. Some of the challenges that shaped conch-shell evolution are the same as those we're facing in designing a bike helmet. Other challenges are different. I can see that you recognize the difference, so I'll leave you to your work."

Ideas-from-nature expert #2 (arriving out of breath): "Sorry I'm late. I just heard the last part of that. I have a different idea. Instead of copying conch shells, what about copying rocks? They've been tested over thousands of years. I know where there's some obsidian that's been exposed to ultraviolet light and erosion for millennia, and it's still there. Maybe your helmet shells should mimic the glass-like structure of obsidian."

Engineer (one week later): "We tested the obsidian. The conch shell is hundreds of times stronger."

Ideas-from-nature expert #2: "Well, how about this sedimentary rock? It's been around for millions of years, so it must be really strong. It has particles of different sizes; maybe you could copy that structure."

Engineer (one week later): "We tested the sedimentary rock, and it's also much weaker than the conch shells."

Ideas-from-nature expert #2: "Hmmm... Why not combine our best ideas? Here's a sedimentary rock that contains conch shells, embedded in inorganic materials. It's been around for millions of years, so it's probably great. We could make bike helmets with little bits of conch-like material, embedded in some rock-like material."

Ideas-from-nature expert #1: "This illustrates two different kinds of testing over time. The structure of the conch shells in the sedimentary rock has been tested and improved by millions of years of indirect competition among conchs having different shell structures. But the organization of the sedimentary rock (the ratio of conch shell to other materials, or whether the conch shell is uniformly distributed or clumped) hasn't been improved by competition with other rocks. By simply persisting over millions of years, the rock passed a weaker kind of test than that imposed on conch shells through competition over millions of years. If reasonable durability were all we needed, it would be safe to conclude that the rock meets that minimum standard. But, in the absence of data, we have no reason to assume that the rock is more durable than some manmade material, like concrete. We would have to run lots of expensive tests to find out. The conch shells, on the other hand, have already been subject to millions of years of comparative tests by sting rays."

Ideas-from-nature expert #2: "OK, then what about land-snail shells? Their structure has been tested by competition (like conch shells), yet they're sometimes exposed to ultraviolet light (like rocks)."

Ideas-from-nature expert #1: "Good idea. Let's explore that option."

Natural selection has tested the adaptations of trees competitively, like conchs. Forests have only been tested by their ability to persist, like rocks. Nature's wisdom may be found more in trees than in forests.