4 ms·

While I like this project, it seems too ambitious for the current state of affairs. Start with counting how many cells of each type are present for various tis

by nonbel 9y ago

While I like this project, it seems too ambitious for the current state of affairs. Start with counting how many cells of each type are present for various tissues. Do this using cadavers of various ages, etc. Pretty much all we have right now for such estimates are totally back of the napkin.

vanderZwan 9y ago
> Start with counting how many cells of each type are present for various tissues. I'm confused: what do you think this project is trying to achieve if not exactly that?
- nonbel 9y ago
  They are planning on sequencing, etc. That is all great but honestly I think it is jumping the gun. I am saying to simply count the cells, so we have the most basic of information. Work on this only really began in 2013...[1] From (quickly) reading their whitepaper it isn't clear to me whether they will even get the count data. [1] https://www.ncbi.nlm.nih.gov/pubmed/23829164 https://www.ncbi.nlm.nih.gov/pubmed/23829164
  - vanderZwan 9y ago
    I'm sorry, maybe I'm missing something but what you're saying is not making any sense to me. Furthermore it gives me the impression you completely misunderstand the biological science behind this project. I thought you meant figure out the number of different types of cells, but you're actually saying counting the numbers of cells of each type? You're putting the cart before the horse, since we haven identified each cell type yet. That's what this project is doing! What does counting cells in tissues even mean here? Which cells? If you can't even tell the cell types apart, what exactly would you be counting? Do you think we already know every kind of cell type and what does? Because we don't. And even ignoring that: say that we figure out the liver has N hundred million cells. On average, because tissue size wildly varies per person. But hey, sure, from a Pure Science perspective we could figure that out. What does that information then tell us? Is it information in any way meaningful? How does counting the number of cells give us a better understanding of what that tissue does? Would you suggest we try to make sense of how countries are organised and what kind of culture they contain by grouping them by population size? Apparently Ghana and Nepal are identical according to this logic, as are Cameroon and Taiwan, and Niger and Sri Lanka[0]. By comparison, determining cell types via gene expression is like measuring education levels and which percentage of the population is in which profession. I don't know about you, but when it comes to making sense of how the body works, my money is on that. [0] https://en.wikipedia.org/wiki/List_of_countries_and_dependencies_by_population https://en.wikipedia.org/wiki/List_of_countries_and_dependen...
    - nonbel 9y ago
      "Type" of cell is a human construct. There is no actual thing as a type of cell, so the list is always complete. People could decide to have more or less types depending on what they are working on, but there is no sense in trying to delineate all the "types". Currently we already have a classification system for cell types that is used to distinguish between different types of cancer. They should use exactly that same system. Of course the numbers will vary by individual. What we want to get is basic upper/lower bounds. It would probably be best to see how well # of cells correlates with weight, skin area, etc and split the data into groups based on whatever easily measured physiological parameter would work best. Once you have number of cells at various ages, then any biological theory that requires the collective activity of many cells will need to be consistent with these values. This can produce a major constraint on much theorizing, especially in areas like cancer. Say you have a theory that cancer is caused by multiple mutations (eg, n = 7) accumulating in a cell lineage. You have other data about mutation rates per basepair per division (eg, p = 1e-8). If this theory is correct you would need a certain number of divisions to explain the curve of cancer incidence by age for that tissue. That number of divisions can be estimated from the difference in number of cells at various ages (or at least we can get some bounds on it by ignoring cell death, etc) and compared to the value required by the cancer theory.
      - vanderZwan 9y ago
        You sound like a phycisist who thinks he can explain the world in terms of spherical cows, asserting a shit-ton of stuff without clear back-up as to why what you state is true, acting as if all kinds of nuanced issues are simple and/or solved problems, and assuming authority over a field you do not seem to be part of. For example: > Currently we already have a classification system for cell types that is used to distinguish between different types of cancer. They should use exactly that same system. Why? You don't give any reason why this classification system is any better than any other. Why would a system of classification of cancers be useful for classifying all other cell types? Actually, asking this question is already giving this statement too much credit: which of the various classification systems are you even referring to[0]? [0] https://www.news-medical.net/health/Cancer-Classification.aspx https://www.news-medical.net/health/Cancer-Classification.as...

by nonbel 9y ago

vanderZwan 9y ago

> Start with counting how many cells of each type are present for various tissues. I'm confused: what do you think this project is trying to achieve if not exactly that?

nonbel 9y ago
They are planning on sequencing, etc. That is all great but honestly I think it is jumping the gun. I am saying to simply count the cells, so we have the most basic of information. Work on this only really began in 2013...[1] From (quickly) reading their whitepaper it isn't clear to me whether they will even get the count data. [1] https://www.ncbi.nlm.nih.gov/pubmed/23829164 https://www.ncbi.nlm.nih.gov/pubmed/23829164
- vanderZwan 9y ago
  I'm sorry, maybe I'm missing something but what you're saying is not making any sense to me. Furthermore it gives me the impression you completely misunderstand the biological science behind this project. I thought you meant figure out the number of different types of cells, but you're actually saying counting the numbers of cells of each type? You're putting the cart before the horse, since we haven identified each cell type yet. That's what this project is doing! What does counting cells in tissues even mean here? Which cells? If you can't even tell the cell types apart, what exactly would you be counting? Do you think we already know every kind of cell type and what does? Because we don't. And even ignoring that: say that we figure out the liver has N hundred million cells. On average, because tissue size wildly varies per person. But hey, sure, from a Pure Science perspective we could figure that out. What does that information then tell us? Is it information in any way meaningful? How does counting the number of cells give us a better understanding of what that tissue does? Would you suggest we try to make sense of how countries are organised and what kind of culture they contain by grouping them by population size? Apparently Ghana and Nepal are identical according to this logic, as are Cameroon and Taiwan, and Niger and Sri Lanka[0]. By comparison, determining cell types via gene expression is like measuring education levels and which percentage of the population is in which profession. I don't know about you, but when it comes to making sense of how the body works, my money is on that. [0] https://en.wikipedia.org/wiki/List_of_countries_and_dependencies_by_population https://en.wikipedia.org/wiki/List_of_countries_and_dependen...
  - nonbel 9y ago
    "Type" of cell is a human construct. There is no actual thing as a type of cell, so the list is always complete. People could decide to have more or less types depending on what they are working on, but there is no sense in trying to delineate all the "types". Currently we already have a classification system for cell types that is used to distinguish between different types of cancer. They should use exactly that same system. Of course the numbers will vary by individual. What we want to get is basic upper/lower bounds. It would probably be best to see how well # of cells correlates with weight, skin area, etc and split the data into groups based on whatever easily measured physiological parameter would work best. Once you have number of cells at various ages, then any biological theory that requires the collective activity of many cells will need to be consistent with these values. This can produce a major constraint on much theorizing, especially in areas like cancer. Say you have a theory that cancer is caused by multiple mutations (eg, n = 7) accumulating in a cell lineage. You have other data about mutation rates per basepair per division (eg, p = 1e-8). If this theory is correct you would need a certain number of divisions to explain the curve of cancer incidence by age for that tissue. That number of divisions can be estimated from the difference in number of cells at various ages (or at least we can get some bounds on it by ignoring cell death, etc) and compared to the value required by the cancer theory.
    - vanderZwan 9y ago
      You sound like a phycisist who thinks he can explain the world in terms of spherical cows, asserting a shit-ton of stuff without clear back-up as to why what you state is true, acting as if all kinds of nuanced issues are simple and/or solved problems, and assuming authority over a field you do not seem to be part of. For example: > Currently we already have a classification system for cell types that is used to distinguish between different types of cancer. They should use exactly that same system. Why? You don't give any reason why this classification system is any better than any other. Why would a system of classification of cancers be useful for classifying all other cell types? Actually, asking this question is already giving this statement too much credit: which of the various classification systems are you even referring to[0]? [0] https://www.news-medical.net/health/Cancer-Classification.aspx https://www.news-medical.net/health/Cancer-Classification.as...