Category Archives: Peer Reviewed Article Review

using CRISPR to create new crops

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This article in Trends in Plant Science (which I know you’ve seen, since it flies off the news stands) argues that CRISPR should be used to create entirely new crops out of wild plants, mimicking the process that created our most common cereal crops over thousands of years.

Of the more than 300 000 plant species that exist, less than 200 are commercially important, and three species – rice, wheat, and maize – account for the major part of the plant-derived nutrients that humans consume.

Plants with desirable traits, such as perennials with extensive root systems and nitrogen-fixing plants, are currently being domesticated as new crops…

Several traits in crops that were crucial for their domestication are caused by mutations that can be reproduced by genome-editing techniques such as CRISPR/Cas9, offering the potential for accelerated domestication of new crops.

breaking the 90 barrier

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The Lancet has an open-access article on projected life expectancies in 35 industrialized countries by 2030. A few interesting findings are that South Korea seems to have some of the longest life expectancies and some of the largest gains in life expectancy among both sexes. South Korean women are projected to be the first to break the barrier of an average life expectancy of 90, with a 50% probability of this happening by 2030. The USA is consistently below the middle of the pack. The good news is that life expectancy is projected to increase in all countries studied, and the gap between men and women is projected to narrow. The graphics in this article are really interesting – I have picked just one below.

http://www.thelancet.com/journals/lancet/article/PIIS0140-6736(16)32381-9/fulltext

Figure 3 from Future life expectancy in 35 industrialised countries: projections with a Bayesian model ensemble

lead, crime and teen pregnancy

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Leaded gasoline peaked around the year I was born, and both crime and teen pregnancy peaked while I was a teenager. I managed to steer clear of these two things (or maybe I left no evidence in either case…), but maybe I would have been the next Einstein if it weren’t for lead, we’ll never know.

Lead Exposure and Behavior: Effects on Antisocial and Risky Behavior among Children and Adolescents Jessica Wolpaw Reyes NBER Working Paper No. 20366 August 2014

It is well known that exposure to lead has numerous adverse effects on behavior and development. Using data on two cohorts of children from the NLSY, this paper investigates the effect of early childhood lead exposure on behavior problems from childhood through early adulthood. I find large negative consequences of early childhood lead exposure, in the form of an unfolding series of adverse behavioral outcomes: behavior problems as a child, pregnancy and aggression as a teen, and criminal behavior as a young adult. At the levels of lead that were the norm in United States until the late 1980s, estimated elasticities of these behaviors with respect to lead range between 0.1 and 1.0.

Maybe we learned our lesson with lead and mercury and have moved on. Or maybe something as bad or worse is hiding in plain site in our consumer products and we just haven’t figured it out yet.

Just for the archives, here is a key 2000 study by Rick Nevin on the subject: How Lead Exposure Relates to Temporal Changes in IQ, Violent Crime, and Unwed Pregnancy.

This study compares changes in children’s blood lead levels in the United States with subsequent changes in IQ, based on norm comparisons for the Cognitive Abilities Test (CogAT) given to representative national samples of children in 1984 and 1992. The CogAT norm comparisons indicate shifts in IQ levels consistent with the blood lead to IQ relationship reported by an earlier study and population shifts in average blood lead for children under age 6 between 1976 and 1991. The CogAT norm comparisons also support studies indicating that the IQ to blood lead slope may increase at lower blood lead levels. Furthermore, long-term trends in population exposure to gasoline lead were found to be remarkably consistent with subsequent changes in violent crime and unwed pregnancy. Long-term trends in paint and gasoline lead exposure are also strongly associated with subsequent trends in murder rates going back to 1900. The Andings on violent crime and unwed pregnancy are consistent with published data describing the relationship between IQ and social behavior. The Andings with respect to violent crime are also consistent with studies indicating that children with higher bone lead tend to display more aggressive and delinquent behavior. This analysis demonstrates that widespread exposure to lead is likely to have profound implications for a wide array of socially undesirable outcomes.

interspecies chimerism, or Dr. Moreau returns

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I only understand a few words of this paper in Cell, like “human”, “pig”, “embryo”, and “implantation”, but they are enough to raise both my eyebrows. I’ll quote the last paragraph of the paper rather than the abstract because it contains a little less jargon. There are some understandable, or possibly hair-raising depending on your point of view, pictures in the paper too.

Interspecies Chimerism with Mammalian Pluripotent Stem Cells. Wu, Jun et al. Cell, Volume 168 , Issue 3 , 473 – 486

The procedures and observations reported here on the capability of human pluripotent stem cells to integrate and differentiate in a ungulate embryo, albeit at a low level and efficiency, when optimized, may constitute a first step towards realizing the potential of interspecies blastocyst complementation with hPSCs. In particular, they may provide a better understanding of human embryogenesis, facilitate the development and implementation of humanized animal drug test platforms, as well as offer new insights on the onset and progression of human diseases in an in vivo setting. Ultimately, these observations also raise the possibility of xeno-generating transplantable human tissues and organs towards addressing the worldwide shortage of organ donors.

Of course rich people are going to have copies of all their vital organs cloned in pigs as soon as this technology is available. And some mad dictator or Bond villain on an island somewhere is going to be breeding pig people. Now speaking of madmen on islands, there was a story about a certain Dr. Moreau…but it was only a story, right?

 “Monsters manufactured!” said I. “Then you mean to tell me—”

“Yes. These creatures you have seen are animals carven and wrought into new shapes. To that, to the study of the plasticity of living forms, my life has been devoted. I have studied for years, gaining in knowledge as I go. I see you look horrified, and yet I am telling you nothing new. It all lay in the surface of practical anatomy years ago, but no one had the temerity to touch it. It is not simply the outward form of an animal which I can change. The physiology, the chemical rhythm of the creature, may also be made to undergo an enduring modification,—of which vaccination and other methods of inoculation with living or dead matter are examples that will, no doubt, be familiar to you. A similar operation is the transfusion of blood,—with which subject, indeed, I began. These are all familiar cases. Less so, and probably far more extensive, were the operations of those mediaeval practitioners who made dwarfs and beggar-cripples, show-monsters,—some vestiges of whose art still remain in the preliminary manipulation of the young mountebank or contortionist. Victor Hugo gives an account of them in ‘L’Homme qui Rit.’—But perhaps my meaning grows plain now. You begin to see that it is a possible thing to transplant tissue from one part of an animal to another, or from one animal to another; to alter its chemical reactions and methods of growth; to modify the articulations of its limbs; and, indeed, to change it in its most intimate structure.

“And yet this extraordinary branch of knowledge has never been sought as an end, and systematically, by modern investigators until I took it up! Some of such things have been hit upon in the last resort of surgery; most of the kindred evidence that will recur to your mind has been demonstrated as it were by accident,—by tyrants, by criminals, by the breeders of horses and dogs, by all kinds of untrained clumsy-handed men working for their own immediate ends. I was the first man to take up this question armed with antiseptic surgery, and with a really scientific knowledge of the laws of growth. Yet one would imagine it must have been practised in secret before. Such creatures as the Siamese Twins—And in the vaults of the Inquisition. No doubt their chief aim was artistic torture, but some at least of the inquisitors must have had a touch of scientific curiosity.”

“But,” said I, “these things—these animals talk!”

He said that was so, and proceeded to point out that the possibility of vivisection does not stop at a mere physical metamorphosis. A pig may be educated. The mental structure is even less determinate than the bodily. In our growing science of hypnotism we find the promise of a possibility of superseding old inherent instincts by new suggestions, grafting upon or replacing the inherited fixed ideas. Very much indeed of what we call moral education, he said, is such an artificial modification and perversion of instinct; pugnacity is trained into courageous self-sacrifice, and suppressed sexuality into religious emotion. And the great difference between man and monkey is in the larynx, he continued,—in the incapacity to frame delicately different sound-symbols by which thought could be sustained. In this I failed to agree with him, but with a certain incivility he declined to notice my objection. He repeated that the thing was so, and continued his account of his work.

I asked him why he had taken the human form as a model. There seemed to me then, and there still seems to me now, a strange wickedness for that choice.

He confessed that he had chosen that form by chance. “I might just as well have worked to form sheep into llamas and llamas into sheep. I suppose there is something in the human form that appeals to the artistic turn more powerfully than any animal shape can.

social interaction in cities

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Here’s an interesting article from the University of Bern, Switzerland, on social interaction in cities. The engineer in me likes to see some hard data and theory applied in the social sciences.

Cities and the Structure of Social Interactions: Evidence from Mobile Phone Data

Social interactions are considered pivotal to urban agglomeration forces. This study employs a unique dataset on mobile phone calls to examine how social interactions differ across cities and peripheral areas. We first show that geographical distance is highly detrimental to interpersonal exchange. We then reveal that individuals residing in high-density locations do not benefit from larger social networks, but from a more efficient structure in terms of higher matching quality and lower clustering. These results are derived from two complementary approaches: Based on a link formation model, we examine how geographical distance, network overlap, and sociodemographic (dis)similarities impact the likelihood that two agents interact. We further decompose the effects from individual, location, and time specific determinants on micro-level network measures by exploiting information on mobile phone users who change their place of residence.

And here’s a more touchy-feely article in Vox on how the U.S. suburban development pattern discourages social interaction.

the key ingredient for the formation of friendships is repeated spontaneous contact. That’s why we make friends in school — because we are forced into regular contact with the same people. It is the natural soil out of which friendship grows…

This kind of spontaneous social mixing doesn’t disappear in post-collegiate life. We bond with co-workers, especially in those scrappy early jobs, and the people who share our rented homes and apartments.

But when we marry and start a family, we are pushed, by custom, policy, and expectation, to move into our own houses. And when we have kids, we find ourselves tied to those houses. Many if not most neighborhoods these days are not safe for unsupervised kid frolicking. In lower-income areas there are no sidewalks; in higher-income areas there are wide streets abutted by large garages. In both cases, the neighborhoods are made for cars, not kids. So kids stay inside playing Xbox, and families don’t leave except to drive somewhere.

I buy this about 75%. I am lucky to live and work in a highly walkable urban neighborhood, and I do have a lot of friendly spontaneous interactions with people around the neighborhood. I have a “scrappy” job where I bond with my co-workers, like soldiers in the trenches. I am also a middle-aged family person and somewhat of an introvert. Part of the reason I don’t have a lot of close adult friendships outside of work and family is that between work and family, I have all the human interaction I can really handle. If I have 15 minutes free on a given day, I would rather spend it alone than interacting with yet another person. I suppose this could change when the kids get a little older and/or when I don’t have to work so much, assuming I live long enough for these things to happen. So I’m just saying there are family pressures, financial and career pressures, and personality differences that influence these things alongside urban form.

Back to the first article, it suggests that high school, college, band camp, and even most workplaces might not be the best model of the most fulfilling and productive social interactions that can develop among adults in the best cities. In high school and college we tend to form small, tight-knit groups where most people in the group network only within the group. The first article above, if I am interpreting it correctly, describes a case where not only are individuals interacting frequently within a social network, but relatively open social networks themselves are interacting with each other as individuals within them interact in random and freewheeling ways. It’s wonderful. Now if you’ll excuse me I’m going to sit on my couch for a little while, watch some TV, unwind and recharge so I can handle the social interaction that will be thrown at me tomorrow.

IBM’s Smarter Cities

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What exactly has IBM been up to all this time with its Smarter Cities program? It’s been hard to figure out. The marketing hype and media coverage have seemed to die down a bit. But here is an article in Cities with some research on it.

An investigation of IBM’s Smarter Cites Challenge: What do participating cities want?

In 2010, IBM created the Smarter Cites Challenge to address critical issues of the 21st century through its digital expertise, in collaboration with city governments. Despite questions about the origin and intentions of IBM’s involvement, 130 cities from all around the world took up the challenge in the first five years. There is limited case study research available on a number of participating cities which has not been able to unpack cities’ rationale for working with IBM. This paper provides an index of all participating cities in the Smarter Cities Challenge, to understand the areas of interest in which urban governments have been seeking IBM’s consulting service. Findings present the state of smart city thinking in urban governments, and raise questions about the multidimensional integration, if any, across the areas of focus in which digital technologies are shaping contemporary cities.

ride pooling can (maybe) reduce traffic by a lot

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Here’s a new study from MIT that says ride sharing and pooling algorithms could theoretically reduce Manhattan rush hour traffic drastically.

On-demand high-capacity ride-sharing via dynamic trip-vehicle assignment

Ride-sharing services are transforming urban mobility by providing timely and convenient transportation to anybody, anywhere, and anytime. These services present enormous potential for positive societal impacts with respect to pollution, energy consumption, congestion, etc. Current mathematical models, however, do not fully address the potential of ride-sharing. Recently, a large-scale study highlighted some of the benefits of car pooling but was limited to static routes with two riders per vehicle (optimally) or three (with heuristics). We present a more general mathematical model for real-time high-capacity ride-sharing that (i) scales to large numbers of passengers and trips and (ii) dynamically generates optimal routes with respect to online demand and vehicle locations. The algorithm starts from a greedy assignment and improves it through a constrained optimization, quickly returning solutions of good quality and converging to the optimal assignment over time. We quantify experimentally the tradeoff between fleet size, capacity, waiting time, travel delay, and operational costs for low- to medium-capacity vehicles, such as taxis and van shuttles. The algorithm is validated with ∼3 million rides extracted from the New York City taxicab public dataset. Our experimental study considers ride-sharing with rider capacity of up to 10 simultaneous passengers per vehicle. The algorithm applies to fleets of autonomous vehicles and also incorporates rebalancing of idling vehicles to areas of high demand. This framework is general and can be used for many real-time multivehicle, multitask assignment problems.

There are plenty of criticisms of this type of study. The major one is that if you make a particular transportation option faster and/or cheaper, economics dictates that people will automatically switch to it from other options over time, eventually making it less fast and/or less cheap until the various modes are balanced again. The study above (based on my quick skim of the abstract) probably took data from one or a few Manhattan rush hours and asked how it could be rerouted in the most efficient possible way. I don’t fault them for doing the study, which is really interesting. The economics and human behavioral feedback loops that happen over longer periods of time just need to be studied too before policy decisions are made based on results like these.

I don’t necessarily want UberPool to be the answer to all our infrastructure problems. I love the idea of subway and above-ground rail and bus rapid transit as much as the next person. But as the opening of the most recent segment of New York subway recently showed us, these projects are taking decades to build in the U.S. and costing enormous amounts of money. Europe and Asia are doing much better than us, so maybe we could learn some lessons from them, but our recent political challenges shed some doubt on the idea that we can improve any time soon. (Europe generally manages to do somewhat better with high-wage union labor, while some Asian countries build extremely cost-effectively by issuing temporary work visas to low-wage labor from developing countries. There are political and moral issues on both ends of this spectrum, obviously, but the point is the U.S. doesn’t do either approach well. Much like our health care system, we spend 2 or 3 or 5 times more than everyone else and get worse results.)

If the criticism of the study I mentioned above is that demand projections made before the new infrastructure options or technologies are in place are not going to be accurate, that criticism certainly applies to a subway system that takes decades to build. The entire population, land use, and employment pattern of the area served could change in that time, not to mention that whatever technology is chosen is almost guaranteed to be obsolete the day operation begins. With the ride-sharing algorithms, even if the projections are wrong at first at least you have a system that should be easy to adapt and tweak over time. I don’t see why public bus systems and bus rapid transit can’t be integrated into a system like this. And if people want a vehicle to themselves for some trips sometimes, the algorithms and pricing schemes should be able to accommodate that. You could even imagine an algorithm managing passenger vehicles, freight and delivery vehicles in urban areas so they are less in conflict with other at various times of day and night. The algorithms could be run by government or non-profit entities if we are really afraid of private control, or private algorithms and entities could be forced to communicate and coordinate with one another.

cheetahs: going…going…gone?

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In today’s depressing conservation news, cheetahs are in serious trouble.

Led by Zoological Society of London (ZSL), Panthera and Wildlife Conservation Society (WCS), the study reveals that just 7,100 cheetahs remain globally, representing the best available estimate for the species to date. Furthermore, the cheetah has been driven out of 91% of its historic range. Asiatic cheetah populations have been hit hardest, with fewer than 50 individuals remaining in one isolated pocket of Iran…

To make matters worse, as one of the world’s most wide-ranging carnivores, 77% of the cheetah’s habitat falls outside of protected areas. Unrestricted by boundaries, the species’ wide-ranging movements weaken law enforcement protection and greatly amplify its vulnerability to human pressures. Indeed, largely due to pressures on wildlife and their habitat outside of protected areas, Zimbabwe’s cheetah population has plummeted from 1,200 to a maximum of 170 animals in just 16 years – representing an astonishing loss of 85% of the country’s cheetahs.

Scientists are now calling for an urgent paradigm shift in cheetah conservation, towards landscape-level efforts that transcend national borders and are coordinated by existing regional conservation strategies for the species. A holistic conservation approach, which incentivises protection of cheetahs by local communities and trans-national governments, alongside sustainable human-wildlife coexistence is paramount to the survival of the species.

So it’s habitat loss and the relentless expansion of the human footprint, again. Are Africans just particularly callous toward the loss of the natural world? No, Africa is just one of the last places a lot of the large, charismatic animals are left. We had them elsewhere, but we have long forgotten them. Solutions exist. But I am in a pessimistic mood right now so I don’t think this time will be different, the declines and collapses will just continue to come faster and be more obvious until maybe some things will be done, but most likely they will be too little, too late. Too little, too late, but better than nothing. How is that for a silver lining?

 

Yellowstone

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David Quammen (author of one of my all-time favorite nonfiction books, The Song of the Dodo: Island Biogeography in an Age of Extinction) has a long article in National Geographic about Yellowstone National Park which touches on some of the same things.

The Greater Yellowstone Ecosystem is bigger than any other park complex in the lower 48 states. And size matters. A resonant study published in the journal Nature back in 1987, by a young ecologist named William Newmark, revealed that among 12 national parks and park complexes in the western United States, all except two had lost mammal species in the years since they had been established, but that Greater Yellowstone, as the largest, had lost fewer species than almost all others. Most of those local extinctions had resulted not from direct human persecution—as the wolves of Yellowstone had been persecuted to oblivion—but from the natural processes of extinction characteristic of islands: When habitat is constrained within a limited area, animal populations remain small, and small populations tend to wink out, over time, because of accidental factors such as disease, fire, hard weather, and bad luck. Greater Yellowstone had lost less of its mammal diversity by natural attrition than had small parks such as Zion, Bryce Canyon, and Mount Rainier. Its size, evidently, had served it well.

Newmark’s original work has been challenged in some particulars during the decades since, but its basic conclusion remains sound: Size matters. The size of the Yellowstone complex helped preserve big, fearsome, wide-ranging, combative animals such as the grizzly, each one of which demands a large territory. No other park in the lower 48, apart from Glacier National Park along Montana’s Canadian border, now supports robust populations of the three greatest living North American carnivores—the grizzly, the wolf, the mountain lion—as well as such other predaceous animals as the wolverine, the coyote, the bobcat, and the red fox. Yellowstone is our wildest park south of the border complex that includes Glacier, in part because it’s our biggest.

The other good thing about geographical bigness is that, besides giving space to large predators with broad territorial needs, it usually encompasses habitat diversity as well as sheer space, thereby sheltering a greater variety of creatures at all levels of size, living all modes of life.

Because I am interested in island biogeography and I like the idea of having seminal papers at my fingertips, I looked up the Newmark article mentioned above.

A land-bridge island perspective on mammalian extinctions in western North American parks
WILLIAM D. NEWMARK
Nature 325, 430 – 432 (29 January 1987); doi:10.1038/325430a0

In recent years, a number of authors have suggested several geometric principles for the design of nature reserves based upon the hypothesis that nature reserves are analogous to land-bridge islands. Land-bridge islands are islands that were formerly connected to the mainland and were created by a rise in the level of the ocean. Land-bridge islands are considered supersaturated with species in that the ratio of island to mainland species numbers is higher than expected from the area of the island. As a result, the rate of extinction should exceed the rate of colonization on a land-bridge island, resulting in a loss of species that is suggested to be related to the size and degree of isolation of the island. If nature reserves are considered to be similar to land-bridge islands, because most are slowly becoming isolated from their surroundings by habitat disturbance outside the reserves, several predictions follow. First, the total number of extinctions should exceed the total number of colonizations within a reserve; second, the number of extinctions should be inversely related to reserve size; and third, the number of extinctions should be directly related to reserve age. I report here that the natural post-establishment loss of mammalian species in 14 western North American national parks is consistent with these predictions of the land-bridge island hypothesis and that all but the largest western North American national parks are too small to retain an intact mammalian fauna.

It’s easy to get depressed. Even if we preserved a lot of big open spaces, left them completely alone, and there were no such thing as pollution or climate change, a smaller nature would still be a less healthy nature. The only silver lining is that if we had a really thorough knowledge of how the shapes of preserved lands and the connections between determine their ecosystem health, we could theoretically come up with land use policies and practices to produce the best possible ecosystem health in the remaining space available.

There is research going on in this area:

A simplified econet model for mapping and evaluating structural connectivity with particular attention of ecotones, small habitats, and barriers
Wei Houa, Marco Neubertb, Ulrich Walzc
Landscape and Urban Planning
Volume 160, April 2017, Pages 28–37

Small habitats and ecotones are recognized as key structures in preserving biodiversity and maintaining landscape connectivity. However, most analyses of landscape pattern have not fully accounted for these elements. This leads to an underestimation of the landscape heterogeneity, especially at the local scale. This research aims to evaluate the structural connectivity for a source habitat (i.e., forest) with particular consideration of the roles of ecotones, small habitats, and barriers. A multi-buffer mapping procedure based on vector data is applied on two comparative test sites for mapping ecological networks (econets) which are composed of forest patches, ecotones, corridors, small habitats, and barriers. On this basis, several indices are proposed for quantitative evaluation of structural connectivity of econets. The application of the indices show that our approach can be useful for analyzing econet connectivity and identifying the roles of critical landscape elements, for example the barriers’ effect on overall forest connectivity. Within an econet, ecotones function as extension of forest edges which can increase the intrapatch connectivity; small habitats play the role of stepping stones which can enhance interpatch connections among forest habitats. The proposed econet model provides a generalized illustration of landscape connectivity and can be used to compare and monitor forest pattern.

clean water is not enough

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This article presents evidence for the expected trend in biodiversity of riparian areas (whether lake, river, stream, etc. I can’t tell from the abstract) in response to urbanization. Large water features might be the one piece of the landscape that urban development has trouble erasing. But by changing the nature of the shoreline and adjacent habitat, you would expect a degradation in ecosystem quality, even if the water quality itself is perfectly fine (which it often is not, of course). The question is, could you design a shoreline and adjacent city that would support a significant fraction of the biodiversity and ecosystem function that was once there? In other words, a smaller nature that is still healthy? Or should we write off the idea of a high-functioning urban ecosystem and focus on protecting more wild areas? Well, I don’t know but I can guarantee that not making a serious attempt at either one will not lead to a good outcome.

Decadal declines in bird abundance and diversity in urban riparian zones, Landscape and Urban Planning, Volume 159, March 2017, Pages 48–61

Urbanization is frequently cited as a major driver of species losses worldwide; however, most studies in urban areas use a space-for-time substitution approach to document effects of urbanization through time. Ultimately, understanding the effects of urbanization on biodiversity requires long-term datasets. We examined long-term changes in bird assemblages at 12 riparian sites in the greater Phoenix metropolitan area and nearby Sonoran Desert region, featuring a range of human modifications and levels of water flow. Riparian areas in arid cities represent a key habitat type that is sensitive to human modification and supports high levels of species diversity. We used long-term data to: (1) explore variation in bird communities as a function of water permanence and degree of human-modification; (2) identify which environmental variables best describe differences found across riparian site types; and (3) assess how riparian bird communities, abundance, and species richness have changed through time. Engineered riparian sites supported more broadly distributed generalists; whereas, natural riparian sites supported more specialists. Sites with perennial flows had more vegetation and water compared to ephemeral sites and engineered sites had more impervious surface compared to natural sites. In nearly all comparisons, bird species richness, diversity, and abundance declined across riparian types during the period of study, even for common species. Bird communities in natural settings have changed more than communities at engineered sites. Overall, the riparian bird community is shifting toward urban dwelling, resident species that are characteristic of riparian sites with less water and more impervious surface.