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IDM Grow VIP Genetic Project Update 2

I’ve been doing further reading of this article (https://www.nature.com/articles/nature11119) and have been trying to run some analysis using the information, which has been difficult. The biggest stumbling block is the incredibly dense documentation for using the various databases; my experiences from corporate life with B2B software is excellent documentation from Google and Amazon where there are excellent examples and people to reach out to. The new documentation is incredible dense and is buried deep in technical journals... a practice that is not common in enterprise software...

Nevertheless, I am getting better at it... but just not there yet. This summer I’m taking a Transcriptonomics course that will expand my abilities to do more quantitative research on this topic and I’m hoping can make it easier to participate. I’m also hoping that the resumption of in-person learning can make it easier to seek out resources to help me with my understanding of some of the problems with interacting with the programs. 

Next year, I’m really hoping to produce some more insights into the genes that actually cause some of the behavior that we have seen in tomato plants beyond some the learnings in the scientific paper cited above. 

I’m really looking forward to connecting with everyone in person. 

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Reflections on 6 Months Garden

The garden I’ve been growing as part of the VIP program has been an absolute joy and a fun experience. I have learned a couple of things from the process as well:

- Many plants have to be started indoors and for several weeks/months before they are strong enough for the outdoor NYC environments. 

- Fertilizers definitely help for growing seedlings

- Heat definitely helps to starts germinations; plants that I let germinate taller up on my bookshelf had a stronger germination

- Taking plants outside too early was a giant mistake; I’ve lost 4 big pots of plants to underestimating how cold it would be in April

- Certain plants handle the cold way better - my radishes were completely unbothered by the cold April weather

I’ve posted some photos below of the plants I’ve been growing!

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Entangled Life

This excerpt was incredible interesting because it showed how ever-present things are that we don’t often expect to be there. Fungi is an especially interesting case because it’s not something that we, as humans, think about often or that comes top of mind.  The practical applications such as penicillin and many of our favorite foods are a result of these small and complex interactions but where I think this passage excels is in pointing out microscopic size and breadth of this class of species. 

Our typical experience thinking of fungi is largely limited to thinking about things like mushrooms but we fail to look inside ourselves to see how fungal networks inside of our “microbiome” affect our mood and are responsible for very much of our ability to survive. The author also does well to challenge the classical definitions of “intelligence” and whether the reasoning that we inscribe only to humans is truly deserved and how if we though of intelligence as a capacity to react to our environment - we might see fungi in a different light. 

The sprinkled anecdotes about the magician and perception of the crowds make the piece quite a fun read and easier to absorb. Along with the tales of how it was like to work with the Dutch scientists and phrases like “wood wide web” made this an enjoyable read.

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Seedbank

This seed bank article was extremely interesting because it highlights the microbiomes that exist everywhere around us. The fact that genetic sequencing was able to change the story and make it affordable to find these micro communities around the seeds just shows how much more the science can reveal around the previously unknown. 

The smallest of fungi may also provide the key to increase the yield from plants in a changing world where the climate is more unpredictable and needs to be heartier in order to be able to adapt to climate change. It just also shows that plants and species that we may have thought to have little use for before may be much more important to our puzzle pieces than we could have ever imagined. 

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Sixth Extinction

This was a more difficult read than some of the other projects - because of how massive the extinction seems to be. The photo of the belly up frogs was especially tough to see because these appear to be things that were once in very high abundance. The scariest part of the read is that amphibians are generally thought to be the hardiest of the general creatures - so if they are having difficulties; this could mean very poor things for others as well; the hesitancy of experts to believe that they were under pressure is an even starker point here. 

This chapter makes it clear that there is some “background extinction rate” which can not be mitigated and that happens over the lifecycle of the planet. The ending of the chapter with the understanding that some of the captured frogs will always be living the remainder of their lives in the frog hotel was very sad. This was not the happiest of reads. 

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Grow update

I’ve been really enjoy learning more about growing plants and hydroponics in the class. A big reason that I joined the program is to get more hands on with growing the actual plants and the professor has made that easy. I’ve been growing tomatoes, kale, lavender, and thyme. The professor has also sent us a hydroponic kit that I’ve set up but have not had any yield (yet - there were some delays in relation to COVID shipping). Through growing and actually planting I’ve grown to learn more about the optimal depths, optimal soil conditions, and more about germination.

I’ve attached some photos of grow so far to showcase the progress so far.

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IDM Grow VIP Genetic Project Update

I’ve begun to explore the nature publication here (https://www.nature.com/articles/nature11119) to try to understand the tomato genome. It’s been a hard read this paper, given that I don’t have too much background in the subject but am now just trying to learn more about it. The parts that I am able to understand is the highlighting of the certain genomic pairs which are responsible for expression within the tomato plant. Most interestingly reading the paper it has dawned on me that an interesting application for this program would be to focus the time on providing better ways of communicating gene expression to a wider audience under the scope of the VIP program - for instance, I’m studying Bioinformatics and am having some difficulty with reading this information; what is the purpose of publishing some of this if it is so dense and inaccessible?

  Some of the interesting findings while reading have been the expression that cause potatoes to have a much sturdier cell wall than tomatoes (tomatoes and potatoes are genetic relatives) and have different pigmentation patterns based on the genes that are expressed. However, the biggest takeaway is when reading a sentence like this (For example, the tomato PSY1 and, to a lesser extent, PSY2 genes are expressed in fruits; however, only Psy1 controls fruit pigmentation (Fig. 3). The Psy1- Psy2 duplication appears to coincide with the Solanum triplication (Supplementary Fig. 16) as are several duplications in the IPP, GGPS, and CHY families. The eudicot-common triplication may have contributed to the expansion to the PSY, GGPS and CYP97 families.) I saw the obvious opportunity in dedicating more time to making this discipline more accessible to everyone.

  I’m still planning on growing the plants and showing how different gene expression  in different settings plays a part in how the plants grow, taste, and yield but am now going to focus on explaining some of the science as well.

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Transforming Detroit

This was an amazing story about how the unique challenges of vacant land in Detroit helped spread the urban farming movement. I was surprised by how much acreage was available in Detroit (size of Manhattan, Boston, San Francisco) for all of the businesses to start up. The marriage of commercial and food problems has been incredible. By spurring the investment in these vacant lots and available labor millions of dollars were able to be generated to earn over seven million dollars for those that still live there. 

I really enjoy stories like this because it shows how food systems can benefit people’s health while sustainably growing the local economy. 

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TED Talk Feedback

This was a very inspiring TED talk about the effects of food deserts. The part about the obesity and diabetes rates are especially striking - I couldn’t believe that the rates were 5X worse than the better off parts of the city. 

The trickle down effects of gardening on children and other people in the community was particularly striking - not just the actual food being grown but also the effect of having people being involved in the community. The stories with the homeless becoming more involved in the community was extremely interesting - the note “if kids grow Kale, they eat Kale!” and “with gardening we can put kids on a different track”. 

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The Social Life of Forests

This article was extremely interesting because it showed how visibly quiet organisms are actually communicating without us knowing. The beginning of the article, with the doubt that the researcher received from her colleagues is indicative of the typical conversation when people miss some of the more interesting parts of ecology by just focusing on yield instead of how these networks are able to communicate and grow effectively. 

The usage of different alarm signals within the networks was most interesting to me because it shows us that trees, although not as emotive as animals to our eyes and ears, use proteins and helper organisms to organize and predict certain activities and dangers. The bit about the rate of metabolic activity and survivorship bias really stood out to me when plants are solitary vs. when they are able to grow in a full ecosystem set up with thousands of signals from trees all around them.

Fundamentally, understanding plants and trees as social creatures instead of solitary organisms is an important take away from this article and should be something that is kept in mind for anyone practicing ecology at any level. My hope would be to understand this communication much more in the future when growing my own plants.

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Vertical Farming Article

This article was extremely insightful about the potential of vertical farming. The eye opening revelation about the control and reliance on specific nutrients when growing using these techniques is what surprised me most - “According to Infarm, each one of these new units uses 95 per cent less water, 99 per cent less space and 75 per cent less fertilizer than conventional land-based farming. “ 

The figures, counterbalanced with the fighting for resources we are experiencing now between countries makes it seem like these sort of techniques are the only viable solutions when looking at the problems we are currently presented with. The fascinating aspect of this potential solution is also that it gives everyone a lot more agency over their own food supply because they control the vertical environment in which it is grown in. 

The last piece that was really exciting was the application of these techniques by restaurants. Provisioning the right ingredients is one of the most difficult parts of cooking and can be made significantly easier by giving restaurants the ability to grow just the right tomatoes, just the right lettuce, or just the right cabbage. 

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Closed System Advantages

This article was an extremely interesting overview of a closed environmental system and the benefits it creates for businesses, the community, and the environment. The key is the elimination of waste that is associated with transportation of energy and goods needed to supply different parts of the business community; this generates over 25% of global emissions today. By building a closed system this community of twenty businesses was able to build a sustainable model for multiple businesses to co-exist together in a sustainable fashion. 

The most novel illustration from this article is that the wastes of one business process can be used as input for other parts of other businesses fairly seamlessly. In other breweries, the spent grain that was mentioned in the article, would need to be transported and would likely be just thrown away with no upside for brewery. In this system, the waste can be used to support a neighboring business and to put some additional revenue into the business generating the “waste”. This approach has both a business win for the producer and the consumer while benefiting the wider community. 

The other outstanding point illustrated in this report is the ability of urban farms to have non-obvious methods of reducing the costs and emissions associated with food transportation while providing a good method for sucking excessive carbon from heavily polluting areas. The technology powering these innovations seems to be fairly mature as well and is capable of feeding the entire population of Montreal with a meager 19 large solar rooftops. 

These systems definitely seem to be the future of agriculture because it’s helping local producers cut transportation waste and provide easy to use waste to nearby businesses that can use the available discharge for the production of their own products.

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IDM grow Test