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Science, Evolved and Reimagined

A_Candle_in_the_Dark_by_soraferret Science is a pretty big deal. Science is the foundation for our civilization. Science is the best method we’ve found to map reality, and take us into the unknown on more than whim and prayer. I don’t agree with those who believe that science drained romance from our understanding of the world around us. I don’t agree with those who assert science is just another superstition. I don’t agree with those who assert that science is a tool of oppression by its nature.

With all that stipulated, science has problems. And that’s because it is a human enterprise. Humans are both the root of science’s problems, and, the source of its solutions. Philosophers can think deeply about how science is done, from Karl Popper to Thomas Kuhn, but high level abstraction has little impact on the day to day practice of science. Science today is social. Individuals work in the context of research groups, and then publish and disseminate their findings across the broader community of peers. The social aspect is why genuine scientific productivity on an international scale is so concentrated in a few nations, above and beyond what you might expect from economic development. The per capita gross domestic product difference between Germany and Italy is significant, but it is dwarfed by the yawning scientific productivity chasm between Germany and Italy in any area of science I am personally familiar with. Science exhibits returns to scale. Who you are around makes you smarter in science.

download This is why Twitter has become such a big deal. It’s a way to enable disintermediation; cutting the middlemen and gatekeepers out of the equation, and ratcheting up on the metabolism of discourse so that it is nearly frictionless. About ten years ago some friends of mine disagreed with a scientific paper in PNAS. They were going to write a response, but didn’t think anyone would pay attention, even if PNAS accepted and published it. So they put up a blog post. Today they would probably start responding on Twitter.

This is relevant because of a controversy that recently erupted over disputes about the results of a major paper from a reputable group. Nature has already reported on this, Potential flaws in genomics paper scrutinized on Twitter. Yoav Gilad, a University of Chicago professor, released some critiques of a high-impact PNAS paper from last December, Comparison of the transcriptional landscapes between human and mouse tissues, on Twitter. The critique is now more fully fleshed out in a paper posted at F1000Research. But what has really gotten peoples’ attention is what Mike Snyder, the last author on the mouse-human transcriptional landscape paper, said in response to the way the critiques were delivered:

Michael Snyder, a geneticist at Stanford University in California and co-author of the original paper, stands by his team’s study and its conclusions and says that Gilad broke the “social norms” of science by initially posting the critique on Twitter. Gilad says that he took to social media to highlight his work, which might otherwise have been overlooked.

Obviously there isn’t a book which outlines the social norms of science. These norms have developed and coalesced implicitly, tacitly, over time. And, they change. It’s no surprise that a lot of people on Twitter are taking Gilad’s side in this. Also, many are giving credit to Snyder’s group for releasing the raw data to Gilad for the reanalysis. If Gilad and company are correct then this is another victory for open(ish) data. Derek Lowe has some reasonable thoughts on the details of how this has been playing out in public. I don’t have much to add.*

But, I do wonder how ephemeral the role of Twitter is going to be in the scientific community. After all, Twitter is not a public utility. It’s a public firm which is traded on the stock market and exists to make a profit and return value to its shareholders. There was a time when AOL, or Myspace, were ubiquitous corners of the internet. Though Twitter allows for a level of disintermediation, to some extent it is a stealth intermediary in and of itself.

The social norms of science are evolving, and the rate of change is increasing. I doubt that this generation shall pass into emeritus before the entire edifice of scholarship as we know it, from publishing status quo to the tenure system, is overturned. Snyder put his finger on the fact that Gilad is likely violating the social norms of science, but those were past norms. Scientists are making it up as they go along right now. Genomics in particular, which is a heavily computational field, with many researchers amenable to data sharing, distribution, and reanalysis, is to some extent going to be a guinea pig for other domains. We’re in a time of change, so likely don’t have the clarity we will in a decade or so, when the current maelstrom will have passed and a new equilibrium attained.

* I didn’t pay much attention to the original paper, so I’m having a hard time understanding how the authors didn’t bother to check for batch effects as some are claiming. Finally, I’ve met Mike Snyder, and he’s a very nice person from what I can tell for how big of a deal he is. I hope this resolves without too many hurt feelings and reputations intact on all sides.

 
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  1. Anonymous says:     Show CommentNext New Comment

    Science is a many-splendered thing, but it is by no means the “foundation of our civilization.” Our civilization is much older than science. Rather than put the cart before the horse, it would be more acurate and insightful to say that science is a product of our civilization.

    Read More
    • Replies: @Anonymous
    O.k., so at some point our civilization became a science-based civilization. Identification of that point in time, though, would be crucial, wouldn't it? Let's say you take Maddison's data on historical GDP and want to define a threshold percentage of total GDP being generated by economic activity that could not be performed without some scientific input. What you get from that is essentially the conventional understanding of civilization since astronomy and complex agriculture co-emerge at the same time. There is just no way of getting around it.
    , @Razib Khan
    our "our civilization", i meant modern human (technological) civilization broadly. consumer society post-malthusian, etc.
    , @Twinkie

    Science is a many-splendered thing, but it is by no means the “foundation of our civilization.” Our civilization is much older than science. Rather than put the cart before the horse, it would be more acurate and insightful to say that science is a product of our civilization.
     
    While I also agree that science is not "the foundation of our civilization," I think science is hardly and merely "a product" of our civilization. We live in an overwhelmingly scientific-technological civilization today (whether we think that's a good thing or a bad thing is another matter and is subject to many complex answers). Although some essence of human life has not changed much since time immemorial (e.g. family), our way of life today has diverged significantly and in numerous ways from the days of the early civilizations. To deny that would be ignoring the reality of the vast achievements (and some highly destructive pitfalls) made possible by modern science.

    As for this statement from Mr. Khan:


    Scientists are making it up as they go along right now. Genomics in particular, which is a heavily computational field, with many researchers amenable to data sharing, distribution, and reanalysis, is to some extent going to be a guinea pig for other domains.
     
    ... I wonder whether this optimism of sorts from him is in large part shaped by the particular part of the scientific endeavor that happens to be his medium. Other parts may be more subject to traditionalism.
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  2. The idea of “The Journal” itself seems mostly to be a scorecard for academic achievement now, rather than the communication device it was created to be.

    I wonder if there is a good history of how letters and letter passers like some of the Bernoulli’s and Marin gave way to actual printed journals. We seem to beat another change point.

    Still there will always need to be group communication in a field, since as you say science is social, but today there are a lot of different possibilities, especially if the achievement part is split from the communication part. From simple things like the arxiv to future Xanadu like curated super-wikis. We will see.

    Personally I always see a place for well edited compilations like journals just to save time for the people in the field.

    Read More
    • Replies: @bob sykes
    Promotion and tenure decisions rely heavily on the number of papers a candidate has in high-impact, prestigious journals. In large measure, this reliance is due to the high degree of specialization among modern scientists and the inability of their own departmental colleagues to understand what they are doing. So, the colleagues (the voting body) rely on the opinions of experts in the candidate's field.

    Because of that, I don't see journals disappearing unless tenure disappears. Even then, even with everyone on short-term contracts, intial hires would require some sort of out-of-department validation. So, journals might outlast tenure.
  3. Anonymous says:     Show CommentNext New Comment
    @Anonymous
    Science is a many-splendered thing, but it is by no means the "foundation of our civilization." Our civilization is much older than science. Rather than put the cart before the horse, it would be more acurate and insightful to say that science is a product of our civilization.

    O.k., so at some point our civilization became a science-based civilization. Identification of that point in time, though, would be crucial, wouldn’t it? Let’s say you take Maddison’s data on historical GDP and want to define a threshold percentage of total GDP being generated by economic activity that could not be performed without some scientific input. What you get from that is essentially the conventional understanding of civilization since astronomy and complex agriculture co-emerge at the same time. There is just no way of getting around it.

    Read More
  4. @Anonymous
    Science is a many-splendered thing, but it is by no means the "foundation of our civilization." Our civilization is much older than science. Rather than put the cart before the horse, it would be more acurate and insightful to say that science is a product of our civilization.

    our “our civilization”, i meant modern human (technological) civilization broadly. consumer society post-malthusian, etc.

    Read More
  5. I’m largely sympathetic to the idea science is more foundational than culture to our civilization. But I’m wondering if you’ve read Robert Lucas on the industrial revolution. The chapter from his “Lectures on Economic Growth” about the industrial revolution is particularly provocative. Though as a collection of lectures some of the chapters are far better than others.

    But a quick search shows Lucas is making a similar point in the middle of this article:
    “What occurred around 1800 that is new, that differentiates the modern age from all previous periods, is not technological change by itself but the fact that sometime after that date fertility increases ceased to translate improvements in technology into increases in population. That is, the industrial revolution is invariably associated with the reduction in fertility known as the demographic transition.”

    https://www.minneapolisfed.org/publications/the-region/the-industrial-revolution-past-and-future

    That is to say, while arguably science or the scientific attitude is foundational, the particulars of the industrial revolution were (in Lucas’ view) about a demographic transition where fertility did not track at the expected Malthusian rate to increased wealth and productivity. And as history now clearly shows, we see this phenomena around education of woman (among many other complicated factors). In a narrow Darwinian sense this is a non-optimal response to a rapidly shifting environment. One where perhaps the status signal system pushed fertility down more rapidly than adaptation could keep up. In some sense we are in a non-malthusian window of opportunity right now. Eventually demographics/selection should respond and we’ll go back to Malthusian as fertility picks up through selection in our far wealthier era. But of course that won’t have time to happen in reality. Long before then we’ll seize control of our genetic destiny through direct decision making.

    Anyway, the point here is you may want to read Lucas on demographic transition as a key aspect of the modern era. Arguably complimentary to your science foundational position, but certainly interesting if you haven’t read it before.

    Read More
    • Replies: @Razib Khan
    yeah, i know this argument, and it's a good point. the key is that we know science => technology => greater endogeneous growth. BUT, there is some poorly understood social phenomenon which leads to demographic transition. our own post-malthusian world may be a transient, even assuming transition to AI, as scarcity is a fact of the universe.
  6. @Nathan Taylor
    I'm largely sympathetic to the idea science is more foundational than culture to our civilization. But I'm wondering if you've read Robert Lucas on the industrial revolution. The chapter from his "Lectures on Economic Growth" about the industrial revolution is particularly provocative. Though as a collection of lectures some of the chapters are far better than others.

    But a quick search shows Lucas is making a similar point in the middle of this article:
    "What occurred around 1800 that is new, that differentiates the modern age from all previous periods, is not technological change by itself but the fact that sometime after that date fertility increases ceased to translate improvements in technology into increases in population. That is, the industrial revolution is invariably associated with the reduction in fertility known as the demographic transition."
    https://www.minneapolisfed.org/publications/the-region/the-industrial-revolution-past-and-future

    That is to say, while arguably science or the scientific attitude is foundational, the particulars of the industrial revolution were (in Lucas' view) about a demographic transition where fertility did not track at the expected Malthusian rate to increased wealth and productivity. And as history now clearly shows, we see this phenomena around education of woman (among many other complicated factors). In a narrow Darwinian sense this is a non-optimal response to a rapidly shifting environment. One where perhaps the status signal system pushed fertility down more rapidly than adaptation could keep up. In some sense we are in a non-malthusian window of opportunity right now. Eventually demographics/selection should respond and we'll go back to Malthusian as fertility picks up through selection in our far wealthier era. But of course that won't have time to happen in reality. Long before then we'll seize control of our genetic destiny through direct decision making.

    Anyway, the point here is you may want to read Lucas on demographic transition as a key aspect of the modern era. Arguably complimentary to your science foundational position, but certainly interesting if you haven't read it before.

    yeah, i know this argument, and it’s a good point. the key is that we know science => technology => greater endogeneous growth. BUT, there is some poorly understood social phenomenon which leads to demographic transition. our own post-malthusian world may be a transient, even assuming transition to AI, as scarcity is a fact of the universe.

    Read More
  7. @Anonymous
    Science is a many-splendered thing, but it is by no means the "foundation of our civilization." Our civilization is much older than science. Rather than put the cart before the horse, it would be more acurate and insightful to say that science is a product of our civilization.

    Science is a many-splendered thing, but it is by no means the “foundation of our civilization.” Our civilization is much older than science. Rather than put the cart before the horse, it would be more acurate and insightful to say that science is a product of our civilization.

    While I also agree that science is not “the foundation of our civilization,” I think science is hardly and merely “a product” of our civilization. We live in an overwhelmingly scientific-technological civilization today (whether we think that’s a good thing or a bad thing is another matter and is subject to many complex answers). Although some essence of human life has not changed much since time immemorial (e.g. family), our way of life today has diverged significantly and in numerous ways from the days of the early civilizations. To deny that would be ignoring the reality of the vast achievements (and some highly destructive pitfalls) made possible by modern science.

    As for this statement from Mr. Khan:

    Scientists are making it up as they go along right now. Genomics in particular, which is a heavily computational field, with many researchers amenable to data sharing, distribution, and reanalysis, is to some extent going to be a guinea pig for other domains.

    … I wonder whether this optimism of sorts from him is in large part shaped by the particular part of the scientific endeavor that happens to be his medium. Other parts may be more subject to traditionalism.

    Read More
    • Replies: @Razib Khan
    biomedical science of the traditional sort is much more traditional, and will take some time. but the same forces of change are operative.
  8. @Twinkie

    Science is a many-splendered thing, but it is by no means the “foundation of our civilization.” Our civilization is much older than science. Rather than put the cart before the horse, it would be more acurate and insightful to say that science is a product of our civilization.
     
    While I also agree that science is not "the foundation of our civilization," I think science is hardly and merely "a product" of our civilization. We live in an overwhelmingly scientific-technological civilization today (whether we think that's a good thing or a bad thing is another matter and is subject to many complex answers). Although some essence of human life has not changed much since time immemorial (e.g. family), our way of life today has diverged significantly and in numerous ways from the days of the early civilizations. To deny that would be ignoring the reality of the vast achievements (and some highly destructive pitfalls) made possible by modern science.

    As for this statement from Mr. Khan:


    Scientists are making it up as they go along right now. Genomics in particular, which is a heavily computational field, with many researchers amenable to data sharing, distribution, and reanalysis, is to some extent going to be a guinea pig for other domains.
     
    ... I wonder whether this optimism of sorts from him is in large part shaped by the particular part of the scientific endeavor that happens to be his medium. Other parts may be more subject to traditionalism.

    biomedical science of the traditional sort is much more traditional, and will take some time. but the same forces of change are operative.

    Read More
    • Replies: @Rick
    The only reason that biomedical science is still a bit traditional, is because it has mostly relied on nonspecific, subjective descriptions that are open to many interpretations.

    We are already well on our way to classifying every possible disease state, and normal variation, with enormous amounts of objective data.

    While an individual patient's data is considered quite private at this time, soon this data will be much more openly shared, perhaps in some vaguely 'anonymous' way between doctors at first. But more likely by patients demanding it and then openly sharing it themselves.

    In any case, this public sharing is what will change biomedical science.
  9. @Markk
    The idea of "The Journal" itself seems mostly to be a scorecard for academic achievement now, rather than the communication device it was created to be.

    I wonder if there is a good history of how letters and letter passers like some of the Bernoulli's and Marin gave way to actual printed journals. We seem to beat another change point.

    Still there will always need to be group communication in a field, since as you say science is social, but today there are a lot of different possibilities, especially if the achievement part is split from the communication part. From simple things like the arxiv to future Xanadu like curated super-wikis. We will see.

    Personally I always see a place for well edited compilations like journals just to save time for the people in the field.

    Promotion and tenure decisions rely heavily on the number of papers a candidate has in high-impact, prestigious journals. In large measure, this reliance is due to the high degree of specialization among modern scientists and the inability of their own departmental colleagues to understand what they are doing. So, the colleagues (the voting body) rely on the opinions of experts in the candidate’s field.

    Because of that, I don’t see journals disappearing unless tenure disappears. Even then, even with everyone on short-term contracts, intial hires would require some sort of out-of-department validation. So, journals might outlast tenure.

    Read More
  10. @Razib Khan
    biomedical science of the traditional sort is much more traditional, and will take some time. but the same forces of change are operative.

    The only reason that biomedical science is still a bit traditional, is because it has mostly relied on nonspecific, subjective descriptions that are open to many interpretations.

    We are already well on our way to classifying every possible disease state, and normal variation, with enormous amounts of objective data.

    While an individual patient’s data is considered quite private at this time, soon this data will be much more openly shared, perhaps in some vaguely ‘anonymous’ way between doctors at first. But more likely by patients demanding it and then openly sharing it themselves.

    In any case, this public sharing is what will change biomedical science.

    Read More
  11. Over my head, but from what I can gather I think Gilad did what he did because even with good criticisms, it is too difficult to get a flawed paper retracted.

    The social aspect is why genuine scientific productivity on an international scale is so concentrated in a few nations, above and beyond what you might expect from economic development. The per capita gross domestic product difference between Germany and Italy is significant, but it is dwarfed by the yawning scientific productivity chasm between Germany and Italy in any area of science I am personally familiar with. Science exhibits returns to scale. Who you are around makes you smarter in science.

    Italy is a odd county. There is rampant nepotism even in the universities, they convicted scientists for failing to predict an earthquake, and the Amanda Knox case raised questions about the competence of forensic DNA analysis in Italy.

    GALILEO famously declared that “science proceeds more by what it has learned to ignore than by what it takes into account”

    .

    Read More

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