model-organism   38

Grown-Ass Dogs Don’t Care About Your Stupid Baby Talk
You know that thing you do where you talk to your dog like it’s a baby? New research shows that puppies respond well to this silly form of speech, but older dogs could give a crap. So, stop doing it when your dog grows up.
news  org:lite  trivia  cocktail  nature  speaking  language  developmental  model-organism  study  summary 
october 2017 by nhaliday
Of mice and men: why animal trial results don’t always translate to humans
It showed that of the most-cited animal studies in prestigious scientific journals, such as Nature and Cell, only 37% were replicated in subsequent human randomised trials and 18% were contradicted in human trials. It is safe to assume that less-cited animal studies in lesser journals would have an even lower strike rate.
news  org:mag  org:edu  science  meta:science  medicine  meta:medicine  model-organism  human-study  homo-hetero  data  pro-rata  org:nat  replication  methodology 
september 2017 by nhaliday
Of Mice and Men | West Hunter
It’s not always easy figuring out how a pathogen causes disease. There is an example in mice for which the solution was very difficult, so difficult that we would probably have failed to discover the cause of a similarly obscure infectious disease in humans.

Mycoplasma pulmonis causes a chronic obstructive lung disease in mice, but it wasn’t easy to show this. The disease was first described in 1915, and by 1940, people began to suspect Mycoplasma pulmonis might be the cause. But then again, maybe not. It was often found in mice that seemed healthy. Pure cultures of this organism did not consistently produce lung disease – which means that it didn’t satisfy Koch’s postulates, in particular postulate 1 (The microorganism must be found in abundance in all organisms suffering from the disease, but should not be found in healthy organisms.) and postulate 3 (The cultured microorganism should cause disease when introduced into a healthy organism.).

Well, those postulates are not logic itself, but rather a useful heuristic. Koch knew that, even if lots of other people don’t.

This respiratory disease of mice is long-lasting, but slow to begin. It can take half a lifetime – a mouse lifetime, that is – and that made finding the cause harder. It required patience, which means I certainly couldn’t have done it.

Here’s how they solved it. You can raise germ-free mice. In the early 1970s, researchers injected various candidate pathogens into different groups of germ-free mice and waited to see which, if any, developed this chronic lung disease. It was Mycoplasma pulmonis , all right, but it had taken 60 years to find out.

It turned out that susceptibility differed between different mouse strains – genetic susceptibility was important. Co-infection with other pathogens affected the course of the disease. Microenvironmental details mattered – mainly ammonia in cages where the bedding wasn’t changed often enough. But it didn’t happen without that mycoplasma, which was a key causal link, something every engineer understands but many MDs don’t.

If there was a similarly obscure infectious disease of humans, say one that involved a fairly common bug found in both the just and the unjust, one that took decades for symptoms to manifest – would we have solved it? Probably not.

Cooties are everywhere.

gay germ search: https://westhunt.wordpress.com/2013/07/21/of-mice-and-men/#comment-15905
It’s hard to say, depends on how complicated the path of causation is. Assuming that I’m even right, of course. Some good autopsy studies might be fruitful – you’d look for microanatomical brain differences, as with nartcolepsy. Differences in gene expression, maybe. You could look for a pathogen – using the digital version of RDA (representational difference analysis), say on discordant twins. Do some old-fashioned epidemiology. Look for marker antibodies, signs of some sort of immunological event.

Do all of the above on gay rams – lots easier to get started, much less whining from those being vivisected.

Patrick Moore found the virus causing Kaposi’s sarcoma without any funding at all. I’m sure Peter Thiel could afford a serious try.
west-hunter  scitariat  discussion  ideas  reflection  analogy  model-organism  bio  disease  parasites-microbiome  medicine  epidemiology  heuristic  thick-thin  stories  experiment  track-record  intricacy  gotchas  low-hanging  🌞  patience  complex-systems  meta:medicine  multi  poast  methodology  red-queen  brain-scan  neuro  twin-study  immune  nature  gender  sex  sexuality  thiel  barons  gwern  stylized-facts  inference  apollonian-dionysian 
september 2017 by nhaliday
I hate every ape I see | West Hunter
Chimpanzees, although expensive, are really useful for medical research, since they’re much closer to humans than any other experimental animal. Yet the Feds are phasing out chimp research, and are sending them off to Club Chimp. Francis Collins, director of NIH, says that “new scientific methods and technologies have rendered their use in research largely unnecessary.” Collins is full of crap, as usual.
west-hunter  scitariat  rant  ideas  science  medicine  model-organism  meta:medicine  realness  westminster  kumbaya-kult  is-ought  people  track-record  commentary  current-events  ethics 
may 2017 by nhaliday
Is soy good or bad for me? | Examine.com
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3076650/
The estimated per capita consumption of soybean oil increased >1000-fold from 1909 to 1999.
https://twitter.com/evolutionarypsy/status/892489043446988800 (increase started during 60s)

Clinical studies show no effects of soy protein or isoflavones on reproductive hormones in men: results of a meta-analysis: https://www.ncbi.nlm.nih.gov/pubmed/19524224
No significant effects of soy protein or isoflavone intake on T, SHBG, free T, or FAI were detected regardless of statistical model.

https://www.ncbi.nlm.nih.gov/pmc/?term=soy+phytoestrogen+men
some good ones:
pros and cons: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3074428/
reproductive consequences: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3443604/
visuospatial memory: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC64558/
reject (in humans)t: https://www.ncbi.nlm.nih.gov/pubmed/19524224

https://discourse.soylent.com/t/soy-in-soylent-2-0/22826/

https://well.blogs.nytimes.com/2013/09/27/ask-well-is-it-safe-to-eat-soy/
A: yes
org:health  q-n-a  explanation  summary  endocrine  science-anxiety  regularizer  nutrition  health  fitsci  metabolic  study  medicine  food  hypochondria  🐸  mena4  public-health  links  search  list  database  multi  meta-analysis  model-organism  human-study  developmental  discussion  poast  gnon  org:rec  data  trivia  scale  pro-rata  trends  rot  visuo  spatial  retention  null-result  twitter  social  commentary  pic  time-series 
may 2017 by nhaliday
Low-Hanging Fruit: Consider the Ant | West Hunter
Which ought to be a reminder that biomimetics is a useful approach to invention:  If you can’t think of anything yourself, steal from the products of evolution.  It’s like an an Edisonian approach, only on steroids.

Along those lines, it is well known, to about 0.1% of the population, that some ants have agriculture. Some protect and herd aphids: others gather leaves as the feedstock for an edible fungus. Those leaf-cutting ants also carry symbiotic fungicide-producing  bacteria that protect against weed fungi [ herbicides invented well before atrazine or 2-4D]  Speaking of, if you really, really want to cause trouble, introduce leaf-cutting ants to Africa.
west-hunter  scitariat  discussion  proposal  low-hanging  innovation  bio  nature  agriculture  technology  ideas  discovery  the-trenches  alt-inst  science  model-organism  track-record 
april 2017 by nhaliday
Genome-Wide Association Study Reveals Multiple Loci Influencing Normal Human Facial Morphology
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0099009
https://twitter.com/dgmacarthur/status/904908988516585472
https://twitter.com/piper_jason/status/905128320869662720
http://www.biorxiv.org/content/early/2017/09/07/185330
https://www.technologyreview.com/s/608813/does-your-genome-predict-your-face-not-quite-yet/

http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1000451
Domestic dogs exhibit tremendous phenotypic diversity, including a greater variation in body size than any other terrestrial mammal. Here, we generate a high density map of canine genetic variation by genotyping 915 dogs from 80 domestic dog breeds, 83 wild canids, and 10 outbred African shelter dogs across 60,968 single-nucleotide polymorphisms (SNPs). Coupling this genomic resource with external measurements from breed standards and individuals as well as skeletal measurements from museum specimens, we identify 51 regions of the dog genome associated with phenotypic variation among breeds in 57 traits. The complex traits include average breed body size and external body dimensions and cranial, dental, and long bone shape and size with and without allometric scaling. In contrast to the results from association mapping of quantitative traits in humans and domesticated plants, we find that across dog breeds, a small number of quantitative trait loci (≤3) explain the majority of phenotypic variation for most of the traits we studied. In addition, many genomic regions show signatures of recent selection, with most of the highly differentiated regions being associated with breed-defining traits such as body size, coat characteristics, and ear floppiness. Our results demonstrate the efficacy of mapping multiple traits in the domestic dog using a database of genotyped individuals and highlight the important role human-directed selection has played in altering the genetic architecture of key traits in this important species.
study  biodet  sapiens  embodied  GWAS  genetics  multi  regularizer  QTL  sex  developmental  genetic-load  evopsych  null-result  nature  model-organism  genomics  twitter  social  scitariat  discussion  publishing  realness  drama  preprint  debate  critique  news  org:mag  org:sci  org:biz 
april 2017 by nhaliday
Cat Ladies | West Hunter
hmm...:
If toxo naturally can make people like cat piss, it’s already preadapted to become (with suitable genetic engineering) the model system for many kinds of infectious behavior modifiers.
west-hunter  sapiens  parasites-microbiome  disease  toxo-gondii  neuro  psychiatry  nature  discussion  commentary  gwern  medicine  🌞  embodied  scitariat  hmm  biotech  biohacking  retrofit  public-health  model-organism  pro-rata  epidemiology  drugs  pharma 
march 2017 by nhaliday
Evolution of sexual asymmetry | BMC Evolutionary Biology | Full Text
Background
The clear dominance of two-gender sex in recent species is a notorious puzzle of evolutionary theory. It has at least two layers: besides the most fundamental and challenging question why sex exists at all, the other part of the problem is equally perplexing but much less studied. Why do most sexual organisms use a binary mating system? Even if sex confers an evolutionary advantage (through whatever genetic mechanism), why does it manifest that advantage in two, and exactly two, genders (or mating types)? Why not just one, and why not more than two?

Results
Assuming that sex carries an inherent fitness advantage over pure clonal multiplication, we attempt to give a feasible solution to the problem of the evolution of dimorphic sexual asymmetry as opposed to monomorphic symmetry by using a spatial (cellular automaton) model and its non-spatial (mean-field) approximation. Based on a comparison of the spatial model to the mean-field approximation we suggest that spatial population structure must have played a significant role in the evolution of mating types, due to the largely clonal (self-aggregated) spatial distribution of gamete types, which is plausible in aquatic habitats for physical reasons, and appears to facilitate the evolution of a binary mating system.

Conclusions
Under broad ecological and genetic conditions the cellular automaton predicts selective removal from the population of supposedly primitive gametes that are able to mate with their own type, whereas the non-spatial model admits coexistence of the primitive type and the mating types. Thus we offer a basically ecological solution to a theoretical problem that earlier models based on random gamete encounters had failed to resolve.

Having sex, yes, but with whom? Inferences from fungi on the evolution of anisogamy and mating types: http://onlinelibrary.wiley.com/doi/10.1111/j.1469-185X.2010.00153.x/full
study  bio  evolution  sex  gender  roots  eden  EGT  dynamical  GT-101  🌞  symmetry  oceans  models  stat-mech  automata  deep-materialism  speculation  gender-diff  explanans  multi  model-organism  empirical  ecology 
march 2017 by nhaliday
An anatomically comprehensive atlas of the adult human brain transcriptome
In each brain independently, 84% of unique transcripts on the microarrays (29,412, referred to as genes for this manuscript) were found to be expressed in at least one structure (91.4% overlap in expressed gene sets between brains), consistent with the percentage of genes expressed in mouse brain by ISH (80%; ref. 1) and fetal human brain by microarrays (76%; ref. 11).
study  bio  sapiens  biodet  genetics  genomics  neuro  model-organism  comparison  GWAS  🌞  neuro-nitgrit 
march 2017 by nhaliday
Bisphenol A (BPA)
Alternatives to BPA containers not easy for U.S. foodmakers to find: http://www.washingtonpost.com/wp-dyn/content/article/2010/02/22/AR2010022204830.html

Food is main source of BPA for consumers, thermal paper also potentially significant: https://www.efsa.europa.eu/en/press/news/130725
New data resulting from an EFSA call for data led to a considerable refinement of exposure estimates compared to 2006. For infants and toddlers (aged 6 months-3 years) average exposure from the diet is estimated to amount to 375 nanograms per kilogram of body weight per day (ng/kg bw/day) whereas for the population above 18 years of age (including women of child-bearing age) the figure is up to 132 ng/kg bw/day. By comparison, these estimates are less than 1% of the current Tolerable Daily Intake (TDI) for BPA (0.05 milligrams/kg bw/day) established by EFSA in 2006.

For all population groups above three years of age thermal paper was the second most important source of BPA after the diet (potentially accounting for up to 15% of total exposure in some population groups).

Among other key findings, scientists found dietary exposure to BPA to be the highest among children aged three to ten (explainable by their higher food consumption on a body weight basis). Canned food and non-canned meat and meat products were identified as major contributors to dietary BPA exposure for all age groups.

Tips for Avoiding BPA in Canned Food: http://www.breastcancerfund.org/reduce-your-risk/tips/avoid-bpa.html

Holding Thermal Receipt Paper and Eating Food after Using Hand Sanitizer Results in High Serum Bioactive and Urine Total Levels of Bisphenol A (BPA): http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0110509

Bisphenol S Disrupts Estradiol-Induced Nongenomic Signaling in a Rat Pituitary Cell Line: Effects on Cell Functions: http://ehp.niehs.nih.gov/1205826/
common substitute for BPA

http://wellnessmama.com/54748/hidden-sources-of-bpa/

Effect of probiotics, Bifidobacterium breve and Lactobacillus casei, on bisphenol A exposure in rats: https://www.ncbi.nlm.nih.gov/pubmed/18540113

What are the sources of exposure to eight frequently used phthalic acid esters in Europeans?: https://www.ncbi.nlm.nih.gov/pubmed/16834635
Food is a main source of DiBP, DnBP, and DEHP in consumers. In this case, consumers have very few possibilities to effectively reduce their exposure.

Are endocrine disrupting compounds a health risk in drinking water?: https://www.ncbi.nlm.nih.gov/pubmed/16823090

How to Avoid Phthalates (Even Though You Can't Avoid Phthalates): http://www.huffingtonpost.com/maia-james/phthalates-health_b_2464248.html
data  org:gov  hypochondria  endocrine  embodied-street-fighting  public-health  news  org:rec  business  tradeoffs  food  multi  study  summary  diet  top-n  org:euro  org:health  nitty-gritty  human-bean  checklists  cooking  embodied  human-study  science-anxiety  sanctity-degradation  intervention  epidemiology  bio  🐸  model-organism  list  health  hmm  idk  parasites-microbiome  street-fighting  evidence-based  objektbuch  embodied-pack  chart  roots  h2o  advice  org:lite  biodet  fluid  left-wing 
january 2017 by nhaliday

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