4/22: Mercedes Pascual

[ehuppert]

Comment below with questions or thoughts about the reading for this week's workshop.

Please make your comments by Wednesday 11:59 PM, and upvote at least five of your peers' comments on Thursday prior to the workshop. You need to use 'thumbs-up' for your reactions to count towards 'top comments,' but you can use other emojis on top of the thumbs up.

[xzmerry]

Thank you for sharing! Though I am not able to fully understand the content, it is interesting to know how immune selection contributes to biological diversity, and look forward to seeing how you leverage network theories to disentangle it. I have never thought that an epidemic can have such an effect.

How should we think of epidemics in the history of evolution? It seems to be beneficial but also with a lot of harm. And I think this question is especially important under the background of COVID-19, to provide us a different perspective of thinking about this pandemic.

Second, whether we can trace the movement of people based on their var genes? As we can detect people's var genes and correlate them with the epidemiological records.

[SoyBison]

Thanks for coming to our workshop! It's really cool to have an evolutionary theorist here, as we usually have sociologists. One of the coolest things about being able to study virus genomes is the fact that we can observe evolutionary pressures and effects in real time. In addition, since a virus is basically just genetic material in a box, in a lot of ways, studying the genomics of a virus is essentially just studying the entire thing.

So my question is, in these cases where malarial strains are highly successful compared to their previous generation, is it possible to look at the environment and identify those viral strategies a priori?

[Tanzi11]

Thank you for your upcoming presentation, Dr. Pascual! I have limited understanding of the material, but with what I have learned about sex differentials, are there differences in immune selection between genders, especially as infections such as malaria affect females severely (although, males and females report similar incidences)?

[MkramerPsych]

Dr. Pascual,

Thank you for sharing your research with us! While genomics and epidemiology are not areas of expertise for me, I found your paper on the evolutionary dynamics of immunity networks fascinating. I have two questions, one at a paper-specific level and one at a more general level. Forgive me if my paper question is simply a result of me not understanding some of the content.

With regards to the CRISPR paper, the network structure you demonstrate seems to rely heavily on the validity of CRISPR immunity as a proxy for natural immunity. Is a CRISPR-derived immunity likely to demonstrate the relatively stochastic behavior seen in natural epidemiological models (drawing on my own limited understanding from reading the COVID literature)?

At a more general level, I am curious if you have any thoughts regarding the presentation of computational work to a non-computational audience. Your papers clearly require a solid foundation in both biology and computation to fully grasp, and I can imagine that this work may be difficult to present. When you present, do you find yourself answering the same methodological questions each time? I am curious as I present my own research to non computationally trained researchers and have had issues summarizing methodology without adding significant tangents to my presentations.

[Yutong0828]

Hi Professor Pascual, It’s great to have you here to introduce us your work! I am excited to learn about how computational methods can be used in ecological studies, though it’s kind of difficult for me to understand the whole study. Please forgive me if I have asked any obvious questions. My first question is about the generalization of the current research results. Considering that the current research is conducted in Ghana, would it be possible that the genetic difference between countries or races may lead to different results? Also, I am interested in how the similar immune selection models can be applied to analyze the spread of COVID-19. Thank you very much!

[chiayunc]

Thank you for coming to our workshop. I have a general question on what are the advantages and properties of network that made you thought of using networks to study the evolution of var repertoire structures? how does network application exceeds traditional methods?

[Lynx-jr]

Hi Doctor Pascual, thanks for coming to our workshop! I had lots of fun reading this paper, for example, the var repertoire dynamics. I have a question based on what Yutong said. Given that west Africa has more unique var genes and south America has less, how does this relate to COVID? How would the number of unique var genes change in general?

[FranciscoRMendes]

Hi Doctor, loved your paper, I have a few questions.

1. I understand the need for the neutral process, what I am less clear on, is how externally valid this process is. If I understand this correctly, someone should be infected with one strain of the parasite to be considered a neutral process ("excluding competitive process between strains"). In your sampling in Ghana did you find any subjects who could count as a "neutral"? What was the neutral process in the empirical data? How would you know a subject has one strain of parasite?
2. Why did you choose a parasitic infection like malaria
3. Finally, "the duration of infection" is a poisson Process, I did not quite get that, is that because it is the outcome of some underlying physical process? I should have thought it would be Markov. Is gene activation/deactivation always a poisson process?

One non-technical question : I come from a place where people get malaria every year and some people never get it (I haven't yet). Could it be because we are asymptomatic but contribute to the genetic diversity of the parasite? I didnt think that a parasitic infection could ever be asymptomatic! Is there any research on why some people dont show any symptoms of these vector borne illnesses?

[Qiuyu-Li]

Thank you for sharing! It’s really cool to study on the evolutionary dynamics of immunity network. Please forgive me if I have asked any obvious questions. How do you isolate the effects of NFDS compared to other mechanisms?

[chrismaurice0]

Thank you for coming to our workshop Dr. Pascual. I am not very familiar with the world of genetics, so my question is more general in nature. How do you see neural models (or other computational models) being used in the future to increase the world's understanding of genes, immunity, and transmission of diseases? How do you hope to build off of this research in future works you have planned?

[mikepackard415]

Thank you for sharing this work! I am very much looking forward to the presentation. I think while the audience in this workshop tends to enjoy thinking about networks, and certainly some of us enjoy thinking about evolutionary theory, we don't have much expertise in epidemiology. With that in mind, I am curious about the extent to which you think evolutionary theory and the network analysis methodologies your research team uses in this paper can map onto social science problems. Do you place much stock into the idea of studying cultural evolution from a multilevel, computational perspective?

[qishenfu1]

Hi Prof. Pascual, thank you very much for your sharing! The same as some other classmates, I am not familiar with the world of ecology and evolution, so my question will also be general. I am curious that, compared with traditional methods, what is the biggest advantage of such computational methods? Moreover, what do you think about the difference between natural science data and social science data? Thank you!

[xxicheng]

Thanks for sharing your amazing work! It's fascinating to learn about network analysis in evolutionary studies. I am wondering about the next step of your research.

[MengChenC]

Hi Dr. Pascual, thank you for sharing your work, and the findings in the paper really bring new insights for the studies of genomics and epidemiology, especially the employment of competitive learning and network analysis for higher dimension exploration. I have a similar question to @Yutong0828, how can this approach identify the nuance between genetic compositions in different regions, ethnicities, populations? And how is your speculation regarding this application in areas outside Ghana? Thank you.

[bakerwho]

Thanks for presenting at our workshop! What are the implications of your research to COVID immunity, or even herd immunity?

[william-wei-zhu]

Thank you very much for sharing your work with us. We look forward to your presentation tomorrow.

[yiq029]

Thanks for presenting such an interesting study at our workshop! The dynamics of network analysis is so interesting. I am looking forward to the presentation~

[linghui-wu]

Thank you Professor Pascual for presenting such exciting work. I am sure the network structure would be thought-provoking for anyone from other social science disciplines who would apply network into their research.

[hesongrun]

thanks for the presentation. Look forward to that!

[yutianlai]

Thanks for your presentation! I'm curious about the application of your research

[YanjieZhou]

Thanks very much for your presentation! I think researching var gene is really an interesting topic and I hope that this research result can expand its application range to Asian areas to prove more about its external validity.

[JadeBenson]

Thanks so much for the interesting research! Do you think these same processes you describe here apply to larger and more evolutionary stable organisms (like animals)?

[ChivLiu]

Thank you for your presentation and article! I am not very familiar with biology, but the network theory you proposed is very interesting to me. It is a little similar to the network theory in Mathematics, and what impact would you think of that could bring to our social science studies?

[WMhYang]

Thank you very much for sharing the paper. As a student major in economics, I encountered a hard time understanding the paper, but the network analysis looks interesting. Would you mind provide more basic background knowledge? Thanks again.

[TwoCentimetre]

I wonder in what scenario this method will be used. Has the result of this research already been applied in practice? I want to know more about how people leverage the result of this research. Thanks.

[timqzhang]

Thank you for your paper ! And look forward to any extension of your methodology to other social science fields.

[a-bosko]

Dear Dr. Pascual,

Thank you for presenting in our workshop this week! It was interesting to learn about non-neutral strain structure and understanding how non-neutral processes structure diversity.

In the article, you mention that the findings provide evidence for the role of frequency-dependent competition as a result of immune selection in the structuring antigen composition in a population of P. falciparum.

It is also mentioned that extreme genetic diversity and intense recombination is needed for immune selection to profoundly structure repertoire diversity. I was wondering if you could elaborate on what you mean by “extreme” and “intense” in these contexts.

Thank you, and I look forward to your presentation!

[mingtao-gao]

Thank you for sharing your work and presentation! It's a great paper of using network analysis to study the evolutionary dynamics of immunity. My question is what are the implications of results to current COVID pandemic?

[sabinahartnett]

Thank you for presenting at our workshop! I am excited to hear more about similar research applying neutral models to the current COVID-19 pandemic or tangential versions that may be relevant.

[wanitchayap]

Thank you for your presentation! It is very cool to see an evolutionary scientist at our workshop! Do you have any opinion on evolutionary research that cannot be done as rigorously as evolution on virus (e.g. evolutionary psych)? Do you think computational method could leverage these research in the same way you do with virus?

[FrederickZhengHe]

Thank you very much for this wonderful paper. It is kinda challenging to understand, so I look forward to your presentation tomorrow to clarify the basic concepts and the main findings!

[NaiyuJ]

Great incorporation of ecology and network analysis. Looking forward to your presentation!

[egemenpamukcu]

Thanks for coming to the workshop Dr. Pascual, looking forward to your presentation.

[bjcliang-uchi]

It is great to see how network analysis is used in evolutionary studies! The paper is far beyond my knowledge so I don't want to venture to comment on it.

[MegicLF]

Thank you for sharing. I wonder why you choose networks to study the evolution of var repertoire structures. Are there any significant advantages?

[Leahjl]

Thank you for sharing your research! I'm curious about the application of network analysis to other fields.

[Jasmine97Huang]

Thank you for speaking to us and looking forward to the presentation!

[Dxu1]

Thank you for sharing your research! I am sure that I did not understand fully, but you mentioned cutting 20% of the links were helpful in network analysis. I wonder how you selected the cutoff. Was it through experiment or through prior knowledge with the genes of the strains?

[Yilun0221]

Thank you so much for the presentation! I am quite amateur to ecology, but I think it is a great field to apply social network! But from my perspective, sometimes it is hard to create a micro-world which is 100% independent of the outside world. I wonder how do you solve this problem in your projects?

[hihowme]

Thanks a lot for sharing your work! I am wondering what do you think could be the takeaways from this research to other fields like economics and business? Thanks a lot!

[vinsonyz]

Thank you for your upcoming presentation, Dr. Pascual! How does the network analysis apply to economics?

[lulululugagaga]

Thanks a lot! My question is the same as @wanitchayap !

[ddlee19]

Thank you for your presentation! What direction is the field of computational ecology moving in?

[zixu12]

Thanks for sharing your work! This really brings me to a new world of knowledge. For social science study, the use of machine learning is quite new and it is also limited in part because machine learning is more powerful in prediction while social scientists also care about causality. I am wondering what is the role of machine learning in the biological study both at the current stage and future? Is there any strength or limitation? Thanks again!

[romanticmonkey]

Thank you so much for your presentation! Could you please introduce some interesting parallelism between the biological/ecological words and the social/human world? I'm conjecturing that a lot of the mechanisms might be similar. (e.g. viral contagion)

[ghost]

Could you please explain negative frequency-dependent selection in more detail?

[YijingZhang-98]

Thank you, Dr. Pascual. This is excellent work and very creative. I just had a hard time understanding it, and maybe it is because I have very few backgrounds in ecology. So I would appreciate it if you could explain some concepts in Ecology in some general words... Thanks!

[kthomas14]

Thank you for sharing your research, Dr. Pascual! I was wondering about the process of using computational and statistical methods to accurately simulate genomic processes in real life applications. Was it difficult adapting mathematical/computational methodology to biological processes?

[k-partha]

Thanks for presenting! I know very little about immunity from an evolutionary perspective, so my question is slightly off-topic. To what extent can we use tools of evolutionary insight to understand the diversity of cultures and other social practices? How well does evolutionary thinking scale from the level of biological responses and adaptations to higher-order social behaviour?

[fyzh-git]

Thank you Prof. Pascual for showing us how the network in genes could help reveal the evidence for non-natural process that shapes the strain structure. Honestly, this topic on ecology and evolution is relatively new, and thus a bit obscure to me. But I still hope to get a better understanding of the methodology that you adopted. So I look forward to your presentation for some more intuitive illustration of the methods as well as the results, and wish to obtain an enhanced understanding on your inspiring work. Sincerely thank you again for presenting in our workshop!