1,356 Matching Annotations
  1. Last 7 days
    1. In contrast, it is the removal of rare taxa that would appear to remove valid data.

      There is no clear consensus on if rare taxa are actually valid or not.

    1. mRNAs triphosphorylated at their 5′ ends.

      Good illustration of the 5' triphosphate in Wikipedia - 5' cap structure ; image

    1. However, few examples of such multi-level regulation have been implemented to date20,21. This has resulted in an unclear picture of how best stringent multi-level control can be achieved and the trade-offs that exist between performance, regulatory complexity, and cellular burden when designing these systems.

      Would have loved to see a better discussion of results from 20 which seems to have a nice emphasis on reducing leak and testing it with highly sensitive protease activity + western blot method

    1. The LasR sensing module includes the gene encoding LasR (BBa_C0078)

      This is wrong part #. It should be BBa_C0179

      C0078 encodes LasI - produces C12 AHL (AI-1)

    1. Others argue for a more ecumenical approach, encouraging researchers to try multiple methods on the same data set.

      This is a disaster of a recommendation and will cause the average scientist to present the method that gave the most favorable conclusions rather than be "more creative and find out why different methods gave different answers"

    1. or replicates, no statistics should be shown, because they give only an indication of the fidelity with which the replicates were created: they might indicate how good the pipetting was, but they have no bearing on the hypothesis being tested6.

      Talking about technical replicates You are advocating for throwing out technical variation and showing only the mean, isn't this misleading as to any issues with reproducibility in the experimental techniques that readers can anticipate?

    1. errors would reflect the accuracy of pipetting, not the reproduciblity of the differences between the experimental cells and the control cells

      It depends on where you believe the differences between replicates are arising from? - When making the mutations - when growing the cells with the mutations

    1. chose the introduction because this section of a paper is fairly easy for ChatGPT to write if it has access to background literature

      Pros and cons of having chatGPT write the introduction - Saves time for researchers ; without too bad of a job - Erodes a vital chance for researchers to deep dive into literature with the deliberate intention of writing - could be helpful in generating new ideas

  2. Nov 2023
    1. rigid pili, such as Inc N, P and W, conjugate at rates 2–4 orders of magnitude higher on solid surfaces
    2. flexible pili (e.g. Inc F, H and I), transfer equally well in liquid as in solid surfaces
    1. synthetic arrays of regulatory RNA could be created that achieved our design goals

      recombinogenic in other organisms?

    1. these commonly used artifacts are small code snippets that are entirely functional in nature and, therefore, when used in isolation, don't enjoy copyright protection at all.

      They are not "used" in isolation though, as it is the context of these code snippets gleaned from tons of code that makes it valuable to the ML scene in comparison to static autocompletion of the prior generation

    1. The donor and recipient populations grow according to the following standard exponential growth equations

      Includes no death rates and carrying capacity. Under what circumstances would this assumption be valid? - if the duration of conjugation (t) is well within the exponential growth phase maybe?

    1. The primary color palette uses three colors. Grey and white should be employed liberally ashigh-contrast elements. Red should be used sparingly to label and decorate symbols and information.We use this pink/red because it is more gender-neutral than the typically masucline color palettes ofother space/geospatial-focused groups and it is distinct from the green/earth tones of conservationgroups. It’s also effective for drawing attention to specific elements

      minimalistic colour palette

    1. apparent permissiveness (AP). It is defined as the ratio of the relative abundance of an ASV in the transconjugant pool to the corresponding recipient pool

      How is this different from conjugation efficiency?

    1. triggering homologous recombination and creating genetic instability10,11,12,13
    2. We applied machine learning to explain how specific interactions controlled the promoters’ transcription rates.

      Is explain the correct word here? - Maybe "fit"?

    1. Wilcoxon rank sum tests were used to test for significant differences between two groups

      Why using non parametric?

    1. Each template molecule in a sample is tagged with a UMI sequence consisting of 10–20 random bases, which can subsequently be used to sort and analyze reads based on their original template molecule

      Key logic that increases accuracy - You are sequencing the same template with the same UMI multiple times (15x here for nanopore) (since it is amplified a bit after the UMI is attached) - Since errors are random, you can bin the molecules with the same UMI (errors in the UMI can be reconciled since the sequences are mapped to the known reference) - Errors are fixed by generating a consensus of things in the same bin - The final UMI consensus error rate is < 0.01% down from 1% (?) in nanopore's native R10.3 technology

    1. Three distinct rRNA sequences exist in the operon, encoding for the two subunits of the ribosome; the 5S and 23S sequences code for the large subunit, while the 16S sequence encodes for the small subunit.

      rRNA operon

    1. demonstrate that targeting of 16S variable regions with short-read sequencing platforms cannot achieve the taxonomic resolution afforded by sequencing the entire (~1500 bp) gene

      Case for nanopore of entire 16S gene (1.5 kb) for better taxonomic resolution

    1. New methods are needed that can manage and help organize this scale of data. To address this, we consider the general problem of computing an approximate distance between two sequences

      the distance is required to search a database for closest entry to a query

    1. we inferred the parameters of a linear function fit to the log transformed gDNA concentration versus detection time (Fig. 2d–g). The inferred slope of the linear function is determined by the cell doubling time (~0.5 h) and intercept is determined by the background mutation frequency

      Interesting.. so it was not from least squares fitting to the data then..

    2. gDNA concentration versus the detection time for the (d) EC sensor, (e) ST sensor, (f) SA sensor and (g) CD sensor

      what is driving these differences? the homology sequence influences the kinetics of recombination?

    3. A threshold of GFP fluorescence 400 arbitrary units (a.u.) was used to determine the detection time for each gDNA concentration.

      what was the basis for this threshold?

    4. expressed from the IPTG-inducible promoter Phyperspank

      what promoter is this? - Bacillus promoter from IGEM, paris 2011

    5. cell-based DNA detection is relatively simple and cost-effective. In comparison, other DNA detection methods such as next-generation sequencing and quantitative polymerase chain reaction require specialized instruments

      Is it simpler to sit and count colonies vs doing qPCR? It is probably cheaper..

    6. Next-generation engineered bacteria hold tremendous promise

      What is specifically next generation? when does this begin?

    1. ubstantial contributions to conception anddesign, or acquisition of data, or analysis andinterpretation of data;

      acquisition of data is an ambiguous phrase here. What if somebody is involved in a preparative protocol where materials are produced but not the acquisition of data?

    1. Your questions should be reasonably scoped. If you can imagine an entire book that answers your question, you’re asking too much.

      hahaha, very useful statement!

  3. Oct 2023
    1. A method was developed for oriented immobilization of bacteriophage T4 through introduction of specific binding ligands into the phage head using a phage display technique

      Why was this method developed?

    1. UMAP embedding of Record-seq data

      Why UMAP for some (4B) and PCA for other dataset (4E)?

    2. metabolites and RNA are short-lived, omics-based measurements of transient stimuli only yield a snapshot of highly dynamic processes.

      Examples of transient stimuli in other context? - In this case, flowing through the intestine with changing conditions makes things transient.

    1. Lactococcal strains were routinely grown in M17 medium (49) supplemented with 1% glucose (GM17 medium) or, when needed, in chemically defined SA medium (26) at 30°C without shaking

      why without shaking?

    1. Acinetobacter baylyi ADP1 (30) and ADP1-ISx (11) were grown at 30°C in LB-Miller (10 g NaCl, 10 g tryptone and 5 g yeast extract per liter) or ABMS minimal medium (40)

      Reference for ADP1-ISx strain

      1. Suárez G.A., Renda B.A., Dasgupta A., Barrick J.E.. Reduced mutation rate and increased transformability of transposon-free Acinetobacter baylyi ADP1-ISx. Appl. Environ. Microbiol. 2017; 83:e01025-17. [PMC free article] [PubMed] [Google Scholar] [Ref list]
    1. a biologically driven cryptic cycle was determined by identifying metabolically active sulfate reducing and sulfur oxidizing lineages co-locating within the sediments, effectively masking sulfide production through re-oxidation back to sulfate.
    1. Corynebacteriumglutamicum

      C. glutamicum is a gram positive of phylum actinomycetatota - 24/Oct/2023

    1. typically between 1010 and 1011 microbial cells per wet-weight gram of faeces7,8,9.
    2. This figure is commonly mentioned in the microbiome literature, but its source has been difficult to ascertain


    3. increased activity has brought with it a degree of hype and misinformation, which can undermine progress and public confidence in the research

      I think any field that has large implications in people's lives - such as food and health are susceptible to misinformation and hype. And it makes is especially complex to debunk when the actual science is too complex to communicate to general public while the field is still in progress

    1. Proteinase K to the reaction to a final concentration of 50–100μg/ml. Incubate at 37–56°C for at least 1 hour. R

      Is 1 hour necessary? The Maxwell protocol DNA Purification from Microorganisms in Water Samples mentions 70C for 10 min with ProK and RNAseA..?

    1. Differences in growth rate, e.g. induced by sub-lethal antibiotic concentrations or temperature, can also significantly bias conjugation rate estimates.

      Do growth conditions bias conjugation rate estimates or do they actually change conjugation rates? - I think it's the latter

    1. The default (50nM) works well with the standard protocol used at the Whitehead/MIT Center for Genome Research

      500 nM each oligo in reaction

    1. a rerun of those identical amplicons (from the same reaction tubes) on a different date yielded “normal” results

      This is scary. How do we trust anything sequencing?

    1. A normal blood sodium level is between 135 and 145 milliequivalents per liter (mEq/L).

      What the fuck are these units? Why not just saw mM?

    1. adjust the sample richness of each ecosystem by adding to it an estimate of the number of unobserved species

      Is this a straightforward thing to do? - Are there any user choices reg distribution etc. that need to be made?

    2. Adjusting for sample size when comparing different groups of observations without discarding data is widely prevalent in the sciences, and discarding data to adjust for unequal sample sizes is the exception

      Ok, I'm sold. No rarefying anymore :P

    3. there is substantial negative bias in the estimates

      rarefaction creates a negative bias?

    4. since estimates for alpha diversity metrics are heavily biased when taxa are unobserved, comparing alpha diversity using either raw or rarefied data should not be undertaken

      Can we say that observing or not of rare taxa depends on the depth of sequencing? (+ other stuff such as lysis method, sample processing etc.)

    5. We currently do not account for measurement error in microbial diversity studies.

      Good point. What do I do with biological replicates?

    6. unique property of microbiome experiments and alpha diversity analysis is that samples do not faithfully represent the entire microbial community under study

      Saying that samples are not representative?

    7. The samples are not of particular interest, except that they reflect the environment from which they were sampled

      Subsampling from a population

    1. Based on these results and well-established statistical theory, we advocate that investigators avoid rarefying altogether. We have provided microbiome-specific extensions to these tools in the R package, phyloseq.
    2. Well-established statistical theory is available that simultaneously accounts for library size differences and biological variability using an appropriate mixture model

      how do we really know what is the appropriate mixture model to use? - Considering that these are to be applied by biologists who are not too well trained in statistics?

      Is there any way to prove that any mixture model performs better than the default rarefaction etc.?

    1. since the most commonly  used models are underdispersed relative to the data, standard errors are almost always zero. The result is that ecologists see incredibly small p values, but replicating results is rare.

      Classical ecology models that work for 100-200 specimens don't work with microbial high throughput sequencing of thousands or millions of sequences, due to their less complexity and the underdispersed nature - Read more about the dispersion

    2. By the way this an example of an excellent lab website/research section with different pointers for different scientific fields and general public also!

    3. We care about producing high-quality software and making our papers reproducible.

      Wonderful :)

    1. the key aspect of a protocol’s ability to accurately reflect the original sample composition can only be assessed with the help of standardized controls like mock communities

      Might be relevant to the RNA memory vs FACS with mock community experimental design of the mock community

    1. sRNAs that repress transcription have been engineered to create orthogonal and composable regulators that can be used to construct RNA-only transcriptional networks
    1. techniques, such as transposition with Mu 11, Tn5 12 and Tn7 13, have been used to add fluorescent gene markers to plasmids

      Read these

  4. Aug 2023
    1. Alongside this, we used pKJK5::gfp, a plasmid lacking these additional payload genes

      review may have asked for this?

    1. none of the organisms identified are known to produce particularly small cells that could pass 0.2 µm filters

      Could broken membrane pieces from dead cells protect the DNA from DNAses?

    1. Nanopore sequencing is used to rapidly and inexpensively assess part composition and create a composition-to-barcode index

      Less coverage needed..

    1. For the terminus, we used primers that amplified part of the dcp gene: 5′-TTGAGCTGCGCCTCATCAAG-3′ and 5′-TCAACGTGCGAGCGATGAAT-3′

      TerC: qPCR copy number of e coli chromosome

    1. Capra Biosciences harnesses the superpowers of a biofilm-forming organism Marinobacter atlanticus to make fat-soluble products like retinol which is used in anti-aging face creams, and high-end industrial lubricants for electric car engines
    2. Some startups, like MicroByre, have been working to domesticate those reluctant, recalcitrant, and rebellious microbes by adapting them for use in the lab and creating genetic tools to manipulate them
    1. Filter and trim

      Also recommended trimleft = 10

      We also choose to trim the first 10 nucleotides of each read based on empirical observations across many Illumina datasets that these base positions are particularly likely to contain pathological errors. Source

      Also note

      Trimming and filtering is performed on paired reads jointly, i.e. both reads must pass the filter for the pair to pass.

      Callahan, Ben J., et al. "Bioconductor workflow for microbiome data analysis: from raw reads to community analyses." F1000Research 5 (2016).

  5. Jul 2023
    1. binding of the Mob protein to the 52-bp sequence could thus allow the formation of a protein-DNA complex with a double function: relaxosome formation andmob gene regulation.

      Mob binds to it's own promoter and represses (negative regulation)

      This is why Mob is preferred in cis for this dual action? - to not make too much mob?

    1. Student's t-Test

      is used to test the (null) hypothesis that two populations have equal means. Source Welch t-test: Wikipedia

    1. approaches, which typically encapsulate bacteria in hydrogels, have produced deployable optical sensors for explosives14, heavy metals15 and chemical inducers16,17
    1. Translocation to a cell’s surface utilizes a signal peptide (for inner membrane translocation) and AIDAc as an outer membrane autotransporter pore
    1. AHL communication modules with functional devices built from the biological components of the las18, tra18, rpa18, rhl19, cin19 and esa20 quorum-sensing systems
    1. Receiver plasmids contained the synthetic PlasR promoter fused to a strong RBS (BBa_B0034) and GFP gene (BBa_E0040) from the IGEM registry. These plasmids additionally contained a pMB1 origin from pET28a and either a chloramphenicol (CmR) or a kanamycin (KanR) selectable marker.

      pSH001 plasmid

  6. Jun 2023
    1. folA gene from the evolved and naive populations was amplified by PCR

      Did you not include the regulatory region?

    2. Evolution in regulatory regions rapidly compensates the cost of nonoptimal codon usage

      Did you observe this effect in the study?

    3. masked by mechanisms affecting the abundance and function of the protein products of the transferred genes downstream to transcription and translation steps, and, therefore, being unrelated to codon bias

      Same effect would also impact this study as well right?

    4. very high antibiotic concentrations used in this study (up to 30-fold the minimal inhibitory concentration [MIC]) potentially minimized the effect of sequence composition on fitness

      Is this by reducing the window of fit phenotypes?

    5. Computational studies that analyzed HGT events among bacterial genomes revealed that HGT frequency positively and strongly correlates with the similarity of tRNA pools between donors and acceptors
    6. 5′-end mRNA, the fitness contribution of mRNA folding stability dominates over that of codon optimality.

      Folding stability is universal between organisms!

    1. We constructed an Escherichia coli donor strain that can deliver a genetic payload into target recipients by broad-host-range bacterial conjugation

      How is this different from MFD-pir?

    2. The mixes were spotted on PBS + 1.5% agar plates and incubated at 37 °C
    1. In contrast, it is the removal of rare taxa that would appear to remove valid data

      So the assumption is that rare taxa are valid? Was this not a point of confrontation with DADA2 people on the merits of alpha diversity measurements?

    1. programming environmental microbes have been applied to a wide range of organisms. Some examples of newly-programmable microbes include

      good citations of engineering non-model organisms

    2. Because biosensors detect at the temporal scales of microbial behaviors, they hold the potential to monitor fast chemical transformations in the environment that are hard to observe, often described as cryptic

      Metabolic reactions such as those involving in iron and sulphur cycling happen at much faster timescales than transcription and translation used by typical biosensors, hence post-transcriptional ones are needed

    3. and AHL controls in this process remain poorly understood.

      This statement should rather say "quorum sensing controls in this process needs more investigation" ; considering that the title of the paper cited says that quorum sensing plays a role in this process?

      Quorum sensing plays a complex role in regulating the enzyme hydrolysis activity of microbes associated with sinking particles in the ocean

      The abstract of the paper says this

      Here, we present data showing that a class of quorum sensing molecules, acylated homeserine lactones (AHLs) substantially impact hydrolytic phosphatase, aminopeptidase, and lipase activity in samples of sinking particles collected from the Atlantic and Pacific Ocean.

    1. instead of being used to endlessly study one environment after another, in situ techniques should be coupled with efforts to model HGT in attached communities by facilitating comparisons between predicted and experimental observations, and assist in establishing predictive frameworks.


    2. Only fluorescence genes have been used for the in situ detection of HGT in natural environments, as no substrate has to be added to detect the product of the expressed reporter gene.

      Is this the only reason? Substrate can be added 1 h prior to the detection to use the other reporter genes for in situ as well right?

    1. The fluorescent marker gene approach is of specific importance in this thesis.Compared to the other reporter gene approaches it allows for quasi-immediate detection of plasmid transfer, even in individual cells, without theneed of substrate addition or taking the strains out of their natural environ-ment.

      interesting point

    1. Christensen et al. (5) which used a specific positive induction of gfp in the recipient rather than a down regulation in the donor as in the system used here.

      From abstract

      gfp gene expressed from the bacteriophage T7 Φ10 promoter on the TOL plasmid, and recipient cells expressing the corresponding phage RNA polymerase

    1. The mobilizing, conjugal plasmid can, now, after retromobilization, co-occurring with RSF1010 in the transconjugant, be subsequently isolated within its original environmental host.

      This is a cool idea!

    2. mobilizable plasmids might less frequently reach dead ends once acquired, since they can utilize the conjugal connections build through adapted resident plasmids in their new host

      What is preventing RP4 from doing the same utilization of conjugal connections of other systems in the new host? Is it less likely because of the larger size?

    1. To date, serine integrases have not been used extensively in plant systems

      although they have been shown to work in principle in Arabidopsis23, Nicotiana benthamiana2421, barley25 and wheat26

    1. Prokaryotic genes are often subjected to frequent horizontal gene transfer [12–16], and one therefore might expect that this could also affect their gene connectivity.

      Is protein protein interaction the most relevant metric of gene connectivity in this context? Would there be other gene network interactions, such as metabolic pathway membership etc. that this matches closer to?

    2. In many cases, such variations reflect differences in the essentiality of genes. Genes with higher connectivity are often more essential for the reproductive success of a cell or organism

      This assumption will not hold true for auxiallary genes or genes not in the core genome but still contribute to essential functions conditional to certain circumstances?

    1. Bacteria evolve rapidly not only by mutation and rapid multiplication, but also by transfer of DNA, which can result in strains with beneficial mutations from more than one parent.

      citable quotes!

    1. conditions amenable to optical outputs for fluorescent reporters, they cannot be applied in native communities growing within non-transparent environmental materials

      This is inaccurate. fluorescent reporters have been used to identify transconjugants in soil and wastewater samples - since cells need to be isolated before the process anyway

    1. Seedlings were transferred to 10-cm square petri dishes containing Fahraeus agar (Somasegaran and Hoben, 1994) covered with sterile filter paper

      Imaging happens within petri dishes

    1. While flowFrame objects store the underlying data matrix inthe exprs slot as an R object, cytoframe objects store the matrix (as well as the data from theother slots) in a C data structure that is accessed through an external pointer. This allows for greateroptimization of data operations including I/O, parsing, transformation, and gating.

      cytoframe vs flowFrame

    1. Collaborative publications, in which the student is one of several authors/creators, are permitted. In every case, the Preface must clearly describe the student's contribution to the research and creation—including, where applicable, the student's role in publications with several authors, or in material created by several authors.
    1. Students enrolled in DSRT 999 are not eligible for the doctoral medical insurance subsidy unless they are otherwise registered as a full-time student.

      how do you register as a full-time student?

  7. May 2023
    1. The dashed lines show the threshold at which cells are considered to be in the ON state (102 for all switches)

      threshold 1e2, seems arbitrary/user determined

    1. cell pellet suspended in 20 μl of Lyse and Go PCR Reagent (Thermo Scientific)

      Does this kind of lysis bias the community to easy lysers? I'm currently just heating 95C, 10 m for lysis and worry about the same.

      Thermo discontinued lyse n go. alternatives? - check Microlysis from gelcompany

    1. at the 100% threshold, microbial diversity could be overestimated by as much as 156.5% when using the full-length gene

      Interesting. Can the species not be resolved with full length 16S as another paper which argued for full length for best resolution?

    1. was digested with PstI (TaKaRa, Japan) to prevent the copy number from being underestimated (66).

      Why does digestion improve the estimation of plasmid vs the chromosome? I would assume the chromosome is more tightly supercoiled and inaccessible unless digested right?

    1. meritocracy is imperfect. The best and brightest do not always win. Butthe idea that meritocracy is nothing but a myth is demonstrably false, indeed absurd

      This article would become supremely lucid if you just took a paragraph to define "merit" according to you.

    2. For science to succeed, it must strive for the nonideological pursuit of objectivetruth.

      Yes, I fully agree. The diversity initiatives are a way to diminish the current biases which are preventing such an objective pursuit of truth

    3. That the absurd comparison of the COVID19 crisis to genocide made it intoprint is consistent with a growing body of evidence suggesting that, in the “right” circles,one can make almost any ridiculous claim, as long as one frames it as advancing “SocialJustice.”

      To me your comparison of diversity initiatives to Lysenkoism is 10 times more egregious

    4. These pieces fail to acknowledge the progress that has been made and continuesto be made toward equality, fairness, and justice throughout the Western world

      yes, that is true. But that doesn't take away from the fact that the scientific comunity and practice still could make a lot more progress on these very objectives. Two things can be true..

    5. typically without citation to supportingevidence

      This would be a valid criticism if indeed true. You also don't give much evidence for your assumptions about objectivity in science and "merit"

    6. But examples of a few overlooked individualsdo not imply that meritbased selection is ineffective—

      Also examples of amazing scientific achievements does not imply that scientific merit of people is in itself an objective measure.

      Your arguments don't live upto the standards you set to the arguments you are attacking

    7. Specifically, he mentions cutoffs thatwould treat 50–75% of applicants as “qualified,” which stops short of abandoning meritaltogether.

      isn't this cutoff a good enough indication of "merit"?

    8. The existence of objective reality, for example,which CSJ denies

      I strongly feel that you are putting words into poor CSJ's mouth but I don't know enough about it to elaborate.

    9. Again, though, the identity or positionality of the mentor is irrelevant tothe evaluation of merit when using these sorts of quantitative metrics.

      In the real world, the personality of the mentor matters a lot to the success of their trainees. And this effect would be a lot more prominent if the evaluation of "merit" would be truely objective and blind to the stellar scientific accomplishments of their mentors - which arguably should have nothing to do with the mentees according to this statement of yours

    10. But the value of just counting, however imperfect, should be obvious

      No. You are comparing just counting to not at all counting as if there was nothing in the middle

    11. The first isthat their rejection of objectivity undermines their credibility. If there is no objectivity, thentheir claims are not objectively true.

      this is a straw man scratching their head and sneezing some words..

    12. These perspectives often view science as a tool of power, are hostile to the centralliberal principle of free inquiry and open discussion, and are closed to calls to justify theirclaims on scientific grounds

      Can both not be possible? Science is liberal and free inquiry and open discussion among the participants and wields power over the non-participants whom it excludes from participation by flawed definitions of "merit"

    13. These core principles, which have served us well for centuries, are under attack byideologies originating in postmodernism and Critical Theory,6,10,14 versions of which rejectobjective reality in favor of “multiple narratives” promulgated by different identity groupsand “alternative ways of knowing.”

      This is a straw-man argument. This is only a small part of a few versions (your words) of critical theory, so cannot be used to discredit the whole thing

    14. Because objectivetruth exists, ultimate consensus among truthseeking actors—scientists—is possible.

      The existence of 'objective truth' means nothing if there are no seekers for it among the scientific community.

    15. we offer a liberal, humanisticalternative that is compatible with maximizing scientific advances.

      I don't see your humanistic alternative; Will read the last part again to make sure

    16. Thestatuses, identities, and demographics of scientists are irrelevant to this great sifting ofvalid versus invalid ideas.

      This is completely untrue. The scientific method is definitely objective but the scientific enteririse is driven by people and incorporates their identities and biases in the kind of questions they even ask. For example, women scientists entering newly in certain fields have started asking questions that haven't been touched so far. For example, they have incorporated the unseen elements of unpaid domestic work in the household as essential elements in macroeconomic thinking.

    17. Fulfilling this responsibility, however, is being hindered by a new, alarming clashbetween liberal epistemology and identitybased ideologies.

      I would love to see evidence for this statement. How exactly is the "objective" pursuit of truth being hindered by social justice and diversity objectives?

    18. How did we get here? Science provided solutions to such calamities as famineand plague, transforming them “from incomprehensible and uncontrollable forces ofnature into manageable challenges.”

      Completely agree. Still have to see how this relates to "merit"


  8. Apr 2023
    1. Don’t waste time and energy collecting metrics you’ll never be able to use. Learn as much as you can from the failures themselves, and then move on.

      The conclusion is illogical and does not follow from the premises. You say that the metrics might not be informative unless there is a model they go with, and now you say to discard metrics altogether rather than have a model.

      And you would also need some metrics collected when failures occur too in order to learn from them right?

    2. Many people rush to collect data without first considering whether they can come up with a model powerful enough to interpret the data. I

      This makes sense

    3. Analysis of your incident data may shed light on your incidents. But incident data really can’t tell you anything about your reliability.

      Aren't these two statements in contradiction?

    1. the diversity of native plants and animals declined with the invasion of alien plants, communities and ecosystems were rarely negatively affected

      Can't make this statement with certainty unless a suite of ecosystem functions were measured..

    2. an alien species is invasive only if it threatens the native biodiversity of recipient ecosystems and negatively affects ecosystem functions, which could lead to detrimental socioeconomic impacts

      needing to have socioeconomic impacts is very narrow minded eh? quite capitalism centric + anthropocentric

    3. most known alien microorganisms are pathogens51, their impact is expected to be negative at all levels.

      Is this a selection effect due to what is studied so far?

      Negative effects are easier to see.. Are they prone to be higher magnitude too?

    4. Several invasive microorganisms infect mainly native plants as their primary host


    1. You cannot claim a credit for education expenses paid with tax-free funds. You must reduce the amount of expenses paid with tax-free grants, scholarships and fellowships and other tax-free education help.

      What are tax-free funds?

    1. transfer efficiencies between them were similar to those seen with parental partners (0.21)

      that is quite high, is this T/D?

    2. The resulting constructs (the pMATING series) could be self-transferred through a variety of prokaryotic and eukaryotic recipients employing such a rationally designed conjugal delivery device.

      eukaryotic is quite surprising. how about gram positives?

    1. Assuming each sequence in our downloaded database represented a unique species

      is the database poor in species resolution? SILVA ssu 99 seems to have good species level annotations

    1. the antagonistic symbiotic relationship between the wasps and their insect hosts allowed the wasp larvae to acquire insect pathogens that subsequently evolved to benefit the wasp

      due to close phylogenetic distance between wasp and the host insect?

    1. Earn 75,000 bonus miles when you spend $4,000 on purchases in the first 3 months from account opening, equal to $750 in travel.

      Sign up before major travel (2,000 $ for 2 people is reasonable in 3 months)

  9. Mar 2023
    1. amperometric sensor was then modified to detect an endocrine disruptor.

      which one? should have been in the abstract

    2. optical signals are often difficult to detect in situ5,6,7,8

      electrical signals easier because the electrical sensors can be miniaturized better?

    1. Some people argue that the Welch’s t-test should be the default choice for comparing the means of two independent groups since it performs better than the Student’s t-test when sample sizes and variances are unequal between groups, and it gives identical results when sample sizes are variances are equal. In practice, when you are comparing the means of two groups it’s unlikely that the standard deviations for each group will be identical. This makes it a good idea to just always use Welch’s t-test, so that you don’t have to make any assumptions about equal variances.
    1. Non-parametric tests don’t make as many assumptions about the data, and are useful when one or more of the common statistical assumptions are violated. However, the inferences they make aren’t as strong as with parametric tests.
    1. In practice, a data set with a sufficient number of replicates forms an approximately normal distribution

      you mean that the <average> of the dataset is normally distributed?

    1. Transcription of the araBAD genes under control of the pBAD promoter is induced about 300-fold above a basal uninduced level within 3 s of the addition of arabinose to cells growing on glycerol in minimal salts medium
    1. This system can efficiently create genome modifications in multiple phages without the need for counterselection

      This implies 100% efficiency? but you are seeing 99% efficiency of single base substitutions only..

      Does this claim make sense?

    1. Nonparametric statistics are often preferred to parametric tests when the sample size is small and the data are skewed or contain outliers.
    2. when to use parametric versus nonparametric tests [8,9,10]
    1. Noteworthy for its longstanding influence is thebook “Nonparametric statistics for the behavioralsciences” by Siege

      Highly cited book from 1956!

      Siegel (1956) pointed out that traditional parametric tests should not be used with extremely small samples, because these tests have several strong assumptions underlying their use. The t-test requires that observations are drawn from a normally distributed population and the two-sample t-test requires that the two populations have the same variance. According to Siegel (1956), these assumptions cannot be tested when the sample size is small. Siegel (1957) stated that “if samples as small as 6 are used, there is no alternative to using a nonparametric statistical test unless the nature of the population distribution is known exactly” (p. 18).

    1. Vmax has a low-level natural resistance to kanamycin but is more susceptible to other antibiotics. When selecting on Kan plates, Vmax with KanR will simply grow faster than Vmax without KanR. Larger colonies=KanR. Other antibiotics select against Vmax but must have a dosage change compared to E. coli.
    2. Wash the culture in fresh LB before adding glycerol, to avoid problems with reviving the culture later

      To prepare V. natriegens cells for −80 °C storage, an overnight culture of V. natriegens was washed in fresh medium before storage in glycerol. Cultures were centrifuged for 1 min at 20,000g and the supernatant was removed. The cell pellet was resuspended in fresh LB3 medium and glycerol was added to 20% final concentration. The stock was quickly vortexed and stored at −80 °C. Bacterial glycerol stocks stored in this manner are viable for at least five years.

      source: Lee, Henry H., et al. "Functional genomics of the rapidly replicating bacterium Vibrio natriegens by CRISPRi." Nature microbiology 4.7 (2019): 1105-1113.