[HN Gopher] Model Organisms Are Not Static
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Model Organisms Are Not Static
Author : mailyk
Score : 31 points
Date : 2025-05-15 15:45 UTC (7 hours ago)
(HTM) web link (www.asimov.press)
(TXT) w3m dump (www.asimov.press)
| pmags wrote:
| This is a real and important challenge, which is even further
| exacerbated if you work on microbial organisms. I can easily
| think of a half dozen times in my own research where we tracked
| down differences in phenotype between ostensibly isogenic strains
| from different labs that turned out to be the result of in lab
| evolution.
| Projectiboga wrote:
| Another influence on that type of research is the diet used,
| those are also standardized and comparisons are only valid if
| comparing the same formula of diet. That also can skew results as
| for example at least one of the formulas is devoid of vitamin e,
| which doesn't really occur in the real world.
| jmward01 wrote:
| I think a better title is 'The world is not static'. I often
| point this out for gradient descent. We always think of the
| static world when envisioning gradient descent but the reality is
| the world is constantly changing and can often actually be
| adversarial. This means that in the long term gradient descent
| can actually select for stability and not optimality in a dynamic
| world (this is where ruts come from I believe). It would be
| interesting to publish an 'expected halflife' statistic for
| scientific knowledge, like biological knowledge, that will change
| over time.
| Feuilles_Mortes wrote:
| _C. elegans_ is nice for this since you can freeze stocks in
| glycerol. Labs routinely go and thaw out the main wild-type
| reference stock if the lab stock has been around for too long.
|
| Now I'm in a fly lab and no one's really figured a good way to
| freeze a fly stock down for long-term storage. So we're left to
| just accept some degree of background mutation and generally
| assume that it's not impacting our experiments _too_ much...
| skeletor_999 wrote:
| It's worth noting that we've found genetic differences between
| the N2 wild type strains used by different labs as well, so
| this is still a problem for C. elegans.
| Feuilles_Mortes wrote:
| biology is hard
| rolph wrote:
| no, biology is fuzzy.
| koeng wrote:
| I do high throughput cloning, so customers of mine want complete,
| verified genes. There is a shit ton of just _stuff_ that can
| happen that you can 't predict even in the most domesticated
| organism.
|
| Most recently, a transposon jumped from E.coli into my backbone,
| and I picked it up during sequence. 6kbp added instantly.
| Absolutely wack.
| DiggyJohnson wrote:
| > Most recently, a transposon jumped from E.coli into my
| backbone, and I picked it up during sequence. 6kbp added
| instantly.
|
| Can you explain this more? Are you referring to your actual
| backbone? How did ecoli meet your backbone and why were you
| sequencing your backbone?
| greazy wrote:
| Backbone refers to the cloning plasmid.
|
| Plasmids are grown inside of bacteria which have their own
| genome with all sorts of oddities like transposons.
|
| Transposons are 'jumping' bits of dna that can insert
| themselves (given the right criteria is met).
|
| So a transposon(s) from the E. coli genome inserted itself
| into the plasmid.
|
| This causes all sorts of problems for people who use them to
| clone (insert) dna into them.
| tehjoker wrote:
| How far are we from being able to synthesize a genome from
| scratch for a small genome organism (or patch a large region)?
| Then we can rely on computer memory.
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