1,501 Matching Annotations
  1. Mar 2020
    1. therefore does not secrete glucose

      Is the glucose secretion low or zero? Does it secrete galactose?

    1. Establishment Democrats are desperately hoping to avoid a reprise of 2016, when Mr. Sanders battled to the bitter end against Hillary Clinton; his posture enraged some in the party who later blamed him for stoking division among Democrats that led to her loss to Mr. Trump.

      Wow! It is the height of foolishness from the establishment democrats if they can still not understand that their moderate-centrist policies are unable to connect with the bulk of the populace, increasingly disillusioned with status quo.

      Unfortunately Bernie wasn't able to do much to broaden the party base as he was tasked to do since 2016. But there was no doubt of his intentions to unite the party when he endorsed Hillary after losing the primary as he said he would this time too. It is just plain undemocratic for the establishment to continue this attitude and blaming any outsiders bringing in new ideas, trying to connect with people (think Ralph Nader) when it is increasingly clear that they are no longer representing priorities important to the electorate.

    1. it is only after the other side has had a chance to put testimony to the test, through cross-examination, that it can be given the status of “evidence”

      Similar to peer review process in science? (probably applicable more so to post-publication review)

    1. The app, which was developed in partnership with a contractor, will run on iPhone 8 devices provided by the bureau

      Why not invest in an android app as well? I would assume it would lead to more widespread use on personal devices

    1. essential functions

      Essentially might not be easily and universally agreed upon

    2. basic infrastructure

      Each and every word of this can be debated upon.

      What comes under basic infrastructure?

      • I presume everyone thinks about high investment hard infrastructure like roads, rail networks, fibre optic and electric lines, airports etc.

      • Are public schools and colleges included?

      • Are medicare and social safety nets counted as basic infrastructure?
      • Is defining criteria of intellectual property and granting patents counted?
      • What about public transportation?
      • Funding early scientific research?

      Or do we expect all of these to be funded through charity?

    1. physically present within the Schengen Area during the 14-day period preceding their entry or attempted entry into the United States.

      Does this include transit through airports on the EU of aliens originating travel from nom-EU locations?

    1. PAM-independent loci were targeted using degenerate codons, thereby making it possible to modify any site in the genome

      From the paper -

      we identified a PAM site in the closest proximity (within the 70 bp coverage of the MAGE oligo) and we introduced a secondary silent mutation that disrupts the nearby PAM sequence while coding for the same amino acid

    1. due to resource constraints, community-level tradeoffs exist between growth yield and resource acquisition, and that nutrient limitation affects community metabolism and reduces growth yield.

      Why should the community come into picture? Individual cell metabolism can also explain reduced growth yield right?

    1. Subsurface drip irrigation provides the ultimate in water use efficiency for open-field agriculture, often resulting in water savings of 25-50% compared to flood irrigation
    1. trace contaminants such as heavy metals in the upper horizons may be accumulated, which may eventually lead to deterioration of soil and groundwater quality and affect the sustainability of land-based disposal of effluent
    1. Eggplant yield under treated effluent was twice the average eggplant production under fresh water irrigation using conventional fertiliser application in Jordan
    1. included bacteria belonging to the Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria classes of proteobacteria

      Does the proteobacterial specificity arise from the RP4 or from the donor being Psuedomonas?

    2. zygotically inducible

      Indicates that expression will occur after conjugation. This term comes from developmental biology field for genes expressed in the zygote - https://en.wikipedia.org/wiki/Maternal_to_zygotic_transition

    1. In situ probes using fluorescence and infrared spectroscopy are also available on the market and have been extensively studied

      Good references for bio-monitoring in situ

      • Purely analytical methods, not biosensors

      Other points from the same paper

      • capable of monitoring the chemical properties of fermentation broths such as biomass, glucose, and protein concentration.
      • infrared spectroscopy can have problems with sensitivity, for low abundance products such as protein products or substrates such as glycerol or glucose.
      • fermentation broths are extremely complex and hence there might be interference?
    1. it is assumed that the decay modifies the growth multiplicatively as a function of the time

      1st order decay

    1. Typically, double terminators are used to stop transcription. Because these parts can be up to ∼168 bp of DNA, this use of double terminators can lead to homologous recombination when used at multiple locations in a design

      double terminators

      Did you test the double terminator strength against your library?

    2. In E. coli, homologous recombination occurs most frequently when there is a contiguous stretch of sequence >25 bp
    1. Exposure to short chain-length AHLs resulted in a decrease in the abundance of different taxa than exposure to higher molecular weight AHLs

      Is there any discussion on how these AHLs are affecting gram positive vs gram negative bacteria?

      • AHLs are linked more often to gram negative bacteria in both production and response, so do they find these connections as well?
  2. Feb 2020
    1. cognizable offence

      What is the definition of a 'cognizable' offense? Are the police allowed to interpret the definition of this term and refuse to file an FIR as we hear in the news on multiple occasions?

      I found a definition and some useful information here - https://www.humanrightsinitiative.org/publications/police/fir.pdf

    1. Don't see the graphic above? Click here.

      What is the connection of these countries to China?

      • Travel?
      • Trade?

      Or is it just a case of random chance?

    1. One return New York-to-London transatlantic flight delivers roughly the same exposure (0.16 mSv) as a nuclear power worker receives in a year (0.18 mSv)

      This is a very interesting fact. Anyone know different sources for this fact?

    1. only

      Only is a strong word, we do not know alternate scenarios

    2. hydro-electric dams are one of the cheapest ways that poor nations can gain access to reliable electricity

      Cheapest way might not be the best or long lasting way

    3. opponents of hydro-electric dams and flood control claim those technologies

      There are lot of shortcomings of large dams - most importantly mass migration of people

    4. not the first time those who are most alarmist about an environmental problem have been most opposed to solving it.

      Maybe the specific olutions you are talking about are being opposed for a reason. This statement is wrong.

      A problem does not have unique solution and opposing bad solutions is as important as finding good solutions or adapting the bad ones to be better

    5. large dams,

      These have a whole slew of problems - especially on overpopulated areas. Look at Narmada river in India

    6. nuclear weapons have contributed to the Long Peace since World War II,

      This is a contentious link between weapons of mass restrictions and peace. Is there wide agreement about this?

    1. produced from abiotic photochemical reduction of Fe(III)-OM, thus closing a cryptic iron cycle under photic conditions

      Is this a significant pathway in a possible cycle in the environment? The photochemical reduction seems quite slow compared to the oxidation, there may be a much faster biotic reduction in the actual envirnoment right. Comments?

    2. Fe(II) concentrations and cell abundances in R. ferrooxidans SW2 growth experiments

      Is this really a cycle? The timescales seem very different

      Fe(2) -> Fe(3) complete in 8 days and growth almost stalls after 14 days. Maybe 8-14 days growth requires the Fe(3) -> Fe(2) step and that's why its a cycle?

    3. Abiotic photochemical reduction of Fe(III).

      Timescales of this reduction are very slow compared to bacterial oxidation

    4. Fe(II) concentrations were determined anoxically using the ferrozine assay

      Can Fe(3) also be determined easily? Would have been good supplementary information to prove that Fe(2) is being converted to Fe(3)

    5. were placed horizontally under a 40-W incandescent light bulb

      Why do you need light for the bacteria to oxidize Fe(2)?

      • Isn't there simultaneous photochemical reduction of Fe(3) happening in this experiment?
    6. 2 mM FeCl2

      Why is this higher than the previous experiment?

      • Previous one was 0.1 mM, this is 2 mM of Fe ions
    7. Oxidation of Fe(II) by R. ferrooxidans SW2

      Does it make sense to fit enzyme kinetics curves to these reactions rather than join the data points?

      • Might be complicated since there are multiple steps involved - Substrate import into cells, Enzymatic degratation

      Also dotted lines are distracting

      • Why didn't you measure Fe(3) concentrations?
    8. guarantees that cells are actively metabolizing but no cell growth is possible, and that therefore, changing cell numbers does not influence the quantification of metabolic rates.

      This will miss any Fe compound induced gene activation a which might give higher rates to the redox reactions.

      • Gene transcription and translation is not as efficient in stationary phase for most growth associated genes
    1. there was no Fe(II) oxidation in the abiotic controls

      This should have been reported for 54 h like the Fe(3) reduction experiment in Fig.2

    1. Commerce follows theland and sea routes of the earth, going to whatever country hasany thing to exchange, be it a monarchy or a republic. Let us bein union with the whole world and not with just a part of it, notwith one part against another.
    1. After many generations in the lab, mice from the desert consumed significantly less water than mice from other localities, indicating that this difference has a genetic basis.

      This could also be explained by epigenetic inheritance. Basically something hereditary - either genetic or epigenetic

    1. all the polling evidence says that America is basically a center-left nation

      But unfortunately Democratic party is dead centre, and does not represent the people as much as it could

    2. is someone who plays right into that strategy, by declaring that he is indeed a socialist.

      Bernie Sanders is championing the causes of the working class and had has always been consistent in his track record. It is justified to fear the ill effects of general perception of 'socialism' but it is high time the americans stop vilifying 'isms' and looking at policies for what they are, the details.

      This column does a very bad job at recognizing working class issues, the same issues that got the republicans into power and Bernie Sanders had the exact mandate to really connect the democratic party with the masses, which I unfortunately think has not been successfully done

    1. But were big banks really at the heart of the financial crisis, and would breaking them up protect us from future crises?

      Yes, keeping investment banking and consumer banking separate is a good idea. Glass Stegall act is a good regulation to do so.

      I heard economists argue on both sides of the spectrum but the main question is why is this article so motivated to paint the Sanders campaign as bad?

    1. same workers in Spain are less equipped to compete for Manufacturing jobs

      But a few highly skilled among them have the possibility of emigrating to Germany?

    2. you might as well get the most productive workers for your “buck”, right?

      I am curious as to why German workers are more productive? Can the other EU nations implement any policies to improve their human resources likewise?

    3. Don’t hate corporations for playing to win — they don’t make the rules, you do.

      Well articulated!

      That reference to computer games is awesome but the problem comes down the the fact that winners of the corporate game are influencing the rules - the corporate tax law, regulations etc.

      Now this is also another problem with how the rulemakers are chosen or how the rules are made. So maybe the solution is to rectify the few rules that influence many other rules being made!

    4. you can’t ever stop because one correction will undo all your spending

      "It is like riding a white tiger" - Byrraju Ramalingaraju. Former chairman of Satyam, convicted of corporate account fudging (a similar game of artificially upholding the value of an entity - except, in this case it was illegal) Source: outlook India

    1. wouldn't you be a fool for not using that move?

      Maybe the game is not exciting anymore if everyone always 'had' to play that move

    1. The researchers from the earlier, statistically significant, study

      Citation?

    1. The host range for three of the plasmids (pBF1, pB7, and pB9) was further investigated by the GFP method described above

      Does the host range of transfer go wider than the population where GFP is observed?

      This is my idea of distinctive overlapping categories of host range as venn diagrams.

    2. Consequently, the plasmid donor cells do not express gfp

      Does the leaky expression not hinder the detecting and quantification of transconjugants in epifluorescence microscopy?

    1. VLPs were discriminated from bacteria or detritus based on pixel dimensions: the pixel area of the smallest known bacterium was established as a maximum cutoff; all objects smaller than this were counted as VLPs.

      Viruses are in size range of 100-500 nm. This is very close to the diffraction limit of light. How is the assumption that anything smaller than bacteria is a virus like particle justified and quantitatively accurate in this regard?

    1. Modeled trends of soil bacterial carrying capacity and diversity are compared to empirical observations

      Isn't this circular logic? The testing empirical data is the same as the data used to build the model

    2. soil becomes sufficiently dry, almost all aqueous habitats are physically isolated and might contain only a few species

      Why is this?

    1. teach science to a general audience

      Aren't most comics based on cultural references like hollywood that are not universal across different cultures and languages. What is a good way to relate to wider general audience?

    1. hypothesized that any single quorum-sensing signal should only induce prophages within a small subset of closely related host bacteria

      This seems like the new thing here compared to Ref 22

    1. scientific laboratories create an amazing amount of plastic waste, consume large amounts of water, create risks from hazardous chemicals and use significantly more energy
    1. plated out on warm agar plates

      It is unclear if the plates contain V2 salts or not

    2. electroporation buffer (680 mM sucrose, 7 mM K2HPO4, pH 7)

      Why not 10% glycerol?

    1. in a pure socialist world everything would be needed to be controlled by the government

      Is this true? I don't know if there is a precise and widely accepted definition of socialism but I would think that socialism is about community ownership of means of production. (I see a complex definition of socialism and capitalism here - https://plato.stanford.edu/entries/socialism/)

      Community can mean the elected government, but in a local sense, it could also be adapted to mean the community that owns, operates, works-in and is frequently served by a given industry. I can think of a simple example of a coffee shop or restaurant in a small town.

    1. Most socialists, however, tend to find the profit motive problematic.

      Is it worthwhile to envision a society where people's motives are pre-anticipated or controllable?

      I think social systems should be robust enough to account for stable functioning of society, independent of the motives and only depending on actions.

      Only actions can be observed, and hence only actions can be regulated in any form of organized society and highly so in capitalism.

    1. socialists do not support capitalism, meaning they want workers to control the means of production

      Workers controlling the means of production sounds like co-operative industries. This paradigm is not antithetical to 'capitalism' in the sense that there is still private ownership of the means of production. I disagree with the statement that democratic socialists do not support capitalism.

      A good debate on this topic here - https://politics.stackexchange.com/questions/323/are-worker-cooperatives-socialist-capitalist-or-their-own-category

    1. whether shared systems of signalling synthesis and degradation

      Do you mean the same organism able to simultaneously perform or switch between the two functions of synthesis and degradation? Or does this mean sharing within the community?

    1. a single-tube, single-step PCR, performed in <2 hours from setup to transformation

      How does the efficiency compare with Gibson assembly and other in vitro methods? Specifically

      • # of colonies
      • Fraction of successful assemblies among the colonies
    1. Rice alumni with accounts on the Alumni Portal are automatically allowed to access a few of the university's licensed electronic resources through the EZproxy server

      Which resources?

    1. Bloom filter
    2. if applied to raw sequence data they would only find matches completely contained within a single read.

      How does the BIGSI method address this concern?

      • Do the k-mers span between reads or
      • Do you make k smaller if there is partial match at the edges of reads?
    3. our use case, where each new microbial dataset brings new variation

      Unlike natural language where vocabulory does not change as new content is added

    4. input data

      The search database - would be a better term

  3. Jan 2020
    1. Transmitting the same power using a higher voltage and lower current loses less of power over the length of the cable. This is more efficient and why the main power grid is hundreds of volts and not 5V.

      A good clarification here on stackexchange - https://electronics.stackexchange.com/a/25571

    1. obtained transcriptional measurements from mid-exponential-phase cultures

      Could be repeated for stationary phase expression?

    1. mobilizable plasmids, possess their own transfer origin and encode a relaxase but need the help of a conjugative plasmid for their transfer from a donor to a recipient

      Why do mobilizable plasmids encode the mob gene? Can't it be provided in trans by the mobilizing helper strain?

    2. Plasmid pBBR1 thus appears to be a new member of this group, even though it resides in gram-negative bacteria and does not replicate via a rolling-circle mechanism
    1. bind the transposon DNA at the flanking inverted repeat sequences, excise the transposon, and paste it into a random TA dinucleotide on a target DNA
    1. stationary-phase cultures grown in rich medium could be refrigerated for more than 1 month without substantial loss of viability

      Barick lab discourages storage at 4C, instead recommending room temperature storage for 2-3 days due to concerns of ROS production. This recommendation was for both plates and liquid cultures

      https://barricklab.org/twiki/bin/view/Lab/ProtocolsWorkingWithVibrioNatriegens

    2. transformation efficiencies were sufficient for routine construction of plasmids from multiple fragments

      How many fragments?

    3. Plasmids with the RK2 replicon could also replicate but were successfully delivered only via conjugation

      Interesting, I wonder why electroporation doesn't work. Does it have something to do with methylation state or other restriction based mechanisms that allow DNA coming in through legitimate means rather than forced means!?

    1. A spacer could compensate for any steric hindrance effect on recruiting the transcriptional machinery at the promoter of the next module in the assembly line; such an effect could be induced by the supercoiling that results when the transcription of the previous module is taking place. However, there is no direct evidence that this may cause a problem, and therefore the argument in favor of using a spacer remains speculative.
    1. As his ideas have permeated the rest of the field, Sanders’s own candidacy appears less radical—or at least less exceptional.

      This is a significant achievement in itself.- Politics is an organized, institutionalized form of conversation and the Bernie 2016 campaign has started the most important conversations in the USA!

    1. . If you are agreeable, you care about your family, your community, society, your country, more than you care about yourself. And if you are disagreeable, then you are a little bit more egotistical.

      This is an interesting categorization. I would assume most people would have some fluidity where people oscillate between these modes according to their life experiences with triggers from the world around them.

    1. do: deregulate, and fast

      deregulation in what aspects? - not all of them are good, certain regulation is necessary and is better for the economy in the long term.This is easier said than done

    2. Gujarat often produced growth faster than the national average, fewer regulations, better infrastructure and less corruption
    1. We are taught that we should be defined by the things other people find impressive, not by the things that bring us joy

      Good point

    1. Get good at knowing what your friends and fans like to see and interact with

      This is just stupid advice. I intend to have an audience in order to read what I write, not the other way around - like Ayn Rand's quote.

    2. he rarely posts status updates and I post pretty frequently and often get good conversations going in the comments.

      Shouldn't rare posts be given higher precedence like twitter does, because rare commodities are more valuable? People who take more time and effort to post valuable content for discussion are bound to post more rarely compared to daily personal updates of what I eat, do etc.

      Twitter notifies me - look at this post, this person has posted something after a long time.

    1. Calling out Uncle Bot’s past vote for Trump threatens his ego and encourages him to double down on his support for the president. Self-esteem is a fundamental human need. If you want people to change their opinion, bolster their ego and help them save face
    2. Fully explore the other person’s perspective before sharing your own to ensure you understand where they are coming from. As with all questions, follow-up inquiries should be nonjudgmental, open-ended and curious.
    1. The concentration of GFP in the sample had been measured using a nanodrop and was ~120μM

      How was the protein quantified? I assume UV absorption or Bradford assay was used.

    1. The fundamental issue surrounding bacterial culture growth measurements is that an absorbance spectrophotometer is being asked to determine light scattering caused by particulates in suspension. In this case, transmittance is not related to absorbance in the classical sense. Under normal true absorbance conditions, spectrophotometers can be comparable to one another because the sample actually absorbs electromagnetic energy. In the case of a reduction of transmittance caused by light scattering, readings are very dependent on the optics of a specific spectrophotometer as well as the cell type in suspension
    2. generally accepted extinction coefficients for nucleic acids are: • Double-stranded DNA: 50 • Single-stranded DNA: 33 • RNA: 40
    1. After all, the rise in antibiotic resistance doesn’t mean that we shouldn’t have invented antibiotics at all.

      It does mean though, that we should try to forsee unintended consequences and not dismiss skeptics without judging the merit of their skepticism with sound scientific discussions. It is famed that Alexander Fleming who discovered the first antibiotic - penicillin, mentioned the observation of resistant bacteria and advised caution in antibiotic usage. This caution went unheeded in the subsequent golden era of antibiotics where all alternatives like phage therapy were shelved from research and development. This is the real lesson we should learn

    2. If a corporation wants to use a gene drive to “cancel out” the herbicide resistance that some weeds have now developed, would that really benefit the planet — or just the corporation that can now sell more of the herbicide that caused the problem in the first place?

      If evolution has any lesson from the development of resistance to the herbicide, it is that some way or other, maybe slower than herbicide resistance, surely the weeds will find a way to subvert any gene drive

    3. With its ability to create powerful changes invisibly, genetic engineering can feel eerie to even the most rational of us

      When things as fundamental as genomes are being modified and amplified through generations, the unforseen consequences have likelihood of being essentially anything. The most rational might be skeptical because of this. Positive feedback system with added noise blows up to infinity or zero; it's an unstable system mathematically

    4. Do we really want the process of scientific research and technology to become democratic — one in which fundamental decisions about public health, like vaccines and vector-control measures, are put up for a vote?

      This is a great debate topic

    5. the lay public’s view is, once you say the person is a scientist, they must know everything.”

      hahaha! so true

    6. and hand control to Big Ag

      How the fuck did big agrobusinesses get so big? Don't these GMO skeptics want to talk about that? About monopolies and anti-trust laws in general? and regulatory capture in other fields as well? Aren't these related issues whereby preventing either of these would have averted the big ag crisis we see today?

      We need discussions around these connected points and not in isolation

    7. s a general idea that these groups aren’t scientific, so their arguments are less valid

      Then the public including the activists and regulatory agents should urgently be 'educated' properly about the technology before moving on to influence their lives irreversibly.

      I believe they are also invited at some of the conferences for such high watch technologies too.

    8. activist groups are more likely to tap into unconscious values and emotions — like using the term “Frankenfoods” to describe G.M.O.s
    9. a misleading focus on “high-profile savior applications” like anti-malarial and conservation efforts

      How is this misleading? Are there any applications that need to be talked about?

    10. compared gene drives to the atomic bomb and accused researchers of using malaria as a Trojan horse to cover up the development of agricultural gene drives for corporate profit
    11. Local and national governments would work with regulatory organizations like the United Nations and the World Health Organization,

      I wish the local and national governments were trustworthy and not corrupted so easily like Monsanto can get them to be

    12. Their financial interest in the intellectual property and their regulatory interest in making sure these products were able to come to market got conflated with the science, so nobody was willing to trust the kind of research they were doing. The end result was that all G.M.O. research got tainted.”

      This speaks volumes of keeping regulatory bodies highly circumspect of lobbyists from the regulated organizations especially when they are near monopolistic.

    13. the technology was controlled primarily by the global agricultural giant Monsanto
    14. struck most people as vaguely creepy
    15. a weapon — say by sabotaging the pollinators that support agriculture, or by altering the genes of innocuous wild insects so they could transmit disease
    16. Could a gene drive stop one virus only to open the way for another, more virulent one? Could it jump from one species to a related one? What would be the environmental effects, if any, of altering the genes of entire species? How about eliminating a species entirely?
    17. Besides combating malaria, gene drives could be used to alter, or even eliminate, other disease-causing insects, from the sand flies that transmit leishmaniasis to ticks that carry Lyme disease in the United States.
    1. power of the people is not only limited to the right of vote, but it extends further and provides us the right to participate in a democratic system by observing, suggesting and discussing, contemplating, questioning, negotiating and dissenting its system or function in various circumstances
    1. CES (combinatorial enhancer solution). 5X CES = 2.7 M betaine, 6.7 mM DTT, 6.7% DMSO, and 55 ug/ml BSA
    2. capable of checking multiple annealing temperatures at a time

      How does this compare with touch up or touch down? Aren't those protocols covering a larger range of temperatures? What are the use cases that differentiate between these two methods

    3. increasing the magnesium concentration, which improves amplification

      Also reduces fidelity?

    4. but the 5’ end is more important

      Do you mean 3'? This is where the extension happens and the GC clamp is recommended

    1. We must stop building new nuclear power plants, and find a real solution to our existing nuclear waste problem.

      We urgently need a debate to discuss and rethink this idea against nuclear energy. I strongly opine that nuclear power generation will be necessary at-least in the short term during the transition into clean energy, hopefully eventually leading to purely sustainable energy and minimizing nuclear energy.

      This article expresses the same point and points out to the German experience of not being able to contain carbon emmissions despite going green energy sans nuclear - https://theweek.com/articles/862988/what-bernie-sanders-elizabeth-warren-wrong-about-nuclear-power

    1. More broadly, we hope that others, especially the hundreds of new startups in synthetic biology, consider sharing pre-competitive ideas, methods, tools, etc. We think the community will be stronger as a result.

      This is a great initiative. Hat's off to this company - Octant-bio for encouraging open sourcing of their hard work and optimization.

    2. we usually need 400-1200 colonies, it’s still easier and faster to do this manually than by colony picker. Also, colony pickers typically cost >$100K and don’t seem appropriate for our scale. 
    3. manually analyzing the data was about as painful as waiting for the results

      I recall someone in Bader lab at JHU had a Perl script to automate alignment of sanger sequencing data; (would be nice to get it onto Github)

    4. OCTOPUS, a light-weight, cost-effective, and robust method for full-plasmid sequence verification using next-generation sequencing
    1. Biosensing intracellular concentrations of metabolites can provide an efficient high-throughput screen of hyperproducing strains.

      bio

    2. Chemical inducers such as carbon sources, metabolites, and antibiotics, environmental signals such as light, pH, oxygen, or temperature, and autoregulatory quorum-sensing molecules can all be sensed by TFs

      Common inducer molecule types

    1. It boils down to priors: do we have reasons to expect large variance in opaqueness? Do we have reason to expect low variance in opaqueness?

      Great point! A lot of debate boils down to competing apriori assumptions by the different parties.

    2. A final word: when we do not understand something, it does not look like there is anything to be understood at all - it just looks like random noise. Just because it looks like noise does not mean there is no hidden structure.

      Excellent statement! Could this be the guiding principle of the current big data boom in biology?

    3. because the receptor both activates and deactivates the internal signal, its concentration cancels out in the equilibrium expression

      Wow!

    1. we were far in advance of Westerners in science and technology at that time.  Today we are far behind them, so what happened?  Why did we not have an Industrial Revolution?  Why did we lag behind?  This is known as Needham’s question or Needham’s Grand Question

      Needham's question

    2. In India, on the other hand, there is tremendous diversity, because whichever group of immigrants came into India brought in their own culture, their religion, their language etc.

      Are there facts supporting the argument that the diversity of India is reflected in the diversity of the incoming immigrants or the source populations? Or is it that the people who settled evolved different cultures and languages on their own?

    1. Nevertheless, fierce Carter administration pressure mounted for him to abdicate.

      This statement is very misleading. It totally misses out the high intensity 1979 Islamic revolution against the Shah, his secret police and favouratist policies, ie) strong factors from with-in Iran that was the actual cause of the 'abdication'

    1. If we reunite, we can pool in our resources and overcome these problems in 15-20 years

      We can say there is a 'possibility' to do it better if we unite, there is no guaranty.

    2. they do not want another China

      China is not an ideal that we want to embrace in this regard, either socio-culturally or economically it is simply not feasible to emulate China given that we are at the brink of industrialization driven global warming and climate change with disastrous consequences

    3. communalism is an artificially-created phenomenon, and can easily be suppressed by a strong secular government.

      That is a very strong assumption and can go either ways.

      Once sown, commununalism can never be sterelized from the population, it will linger on as radical extremist movements continuing to draw support and sympathies. This might be a tiny fraction of the population that can be dismissed as irrelevant or it can amplify and destabilize any 'artificially' created united government as well.

    1. Interactions between Mycobacterium tuberculosis (Mtb) and human (players) are often included in the Mtb’s strategies to invade host responses, to replicate and persist within the host,

      Does the M.Tb have knowledge of the host responses or is it merely adapting bet hedging strategies (a mix of multiple strategies across population) and whatever survived is what we see.

      This will have major implications in treating the problem in a game theoretic fashion

    1. Borate, which is present in LB and SB, causes reversible crosslinks with DNA, reducing the separation of larger DNA fragments unless low % gels are made of high-strength agarose
    1. use of the strong UAAU signal in highly expressed genes and for the occurrence of the weaker UGAC signal at several recording sites.

      three types of recoding events: stop-codon readthrough, –1 ribosome frameshifting and translational bypassing

      (Rodnina, Marina V., et al. "Translational recoding: canonical translation mechanisms reinterpreted." Nucleic acids research (2019).)

    1. suggestive of protein extension, especially at UGA codons, which rely exclusively on the reduced function RF2 variant of the K-12 strain for termination
    1. Since capitalists make money from every hour of workers’ labor, they will get increasingly rich over time, while workers won’t because they’re too busy making money for capitalists

      This is not entirely obvious, it depends on the competing interests of the owners of the means of production vs the workers. The current economic and social organization that disincentivises labour unions and any forms of collective organization on the worker side reduces their bargaining power and hastens this statement. But there can be alternative ways of structuring companies and the macroeconomics to balance both the forces.

      Am I missing something here?

    2. the rich pocket, rather than reinvest, their tax cuts

      Or they reinvest a smaller than expected fraction of it?

      It would be great to see some data on this as the intuition can go both ways. One argument says -

      • Rich do not pocket their wealth, they spend it on overpriced luxury items and long term invesents (really?), whereas working class people spend it in short term purchases for livelihood which does not have as much of a ripple effect on the economy.
  4. Dec 2019
    1. should reject the influence of both liberal capitalism and communism, ideas that inspired the revolutionary slogan "Neither East, nor West – Islamic Republic!"

      In a post cold-war world, viewed in increasing binaries of left and right winds be it social liberal - conservative or socialist-capitalist tendancies, it seems incomprehensible as to how one can reject both USA's and Soviet's socio-economic models. I'm curious to know how they organize their economy in this case.

      One part why the western world hates the Islamic revolution might be their lack of understanding about this exact phrase, other than the fact that Iran became a theocracy.

    1. Religious conflict in any form is often far more impervious to pragmatic solutions, and can prove more dangerous than national conflicts.

      This is debatable. National identity and religion are often both entwined in complex historical factors quite like Judaism and the land of Judea. Whereas national identity is more moldable and dynamic when combined with democratic developments like the Arab spring, religious identity would change slower and might be more important to guard for the conservatives (I'm not sure on this, but it's a gut feeling)

      In such a case, conflicts are easier to understand when cast in terms of religious or sub-religious basis but I definitely think a purely religious conflict (an ideal construct) is more likely to find a pragmatic solution, although I doubt if any thing of that sort exists!

    1. A single transformant may have a mutation at a low level that will eventually sweep through the population

      How does transforming a pure plasmid (miniprep) produce a mixed population?

      • Is a single colony on the transformation plate not really clonal due to evolution occurring in growth from the single founder cell?
      • And also the outgrowth steo prior to plating is introducing additional variation that differentiates different colonies
      • Hence adding these two statements together, picking 3 colonies from a plate streaked from a glycerol stock (derived from a clonal population) has lower variability than 3 colonies picked from a fresh transformation?

      Does this make any suggestion of using one or the other method for generating independent biological replicates?

    2. promoter mutations remove the metabolic load at both the transcriptional and translational levels

      Is there any other sequence dependent feature that might explain why promoters are more predisposed to mutation than RBS?

    3. in the normal MG1655 strain that does not overproduce LacI

      Should have knocked out the LacI for a more robust constitutive activity?

    4. a few simple design principles: high expression of genetic circuits comes with the cost of low evolutionary stability, avoid repeated sequences, and the use of inducible promoters increases stability. Inclusion of an antibiotic resistance gene within the circuit does not ensure evolutionary stability.
    1. Engineering as a practice has not, however, been successful in such endeavors as controlling the weather or avoiding natural disasters, due largely to the scale, complexity and uncertainty inherent to those problems. So we must ask: is the conventional paradigm of engineering appropriate for biology?

      Great point!

    1. CRISPRi-ME prevents evolutionary failure of a burdensome plasmid in E. coli.

      It reduces the rate of evolutionary failure but does not prevent

    1. SDS in loading buffer may contribute to band smearing in precast GelRed® gels. If this occurs, we recommend using the post-staining protocol
    1. 50 μg/ml RNase (ThermoFisher #EN053) freshly added. 2 ml of lysis buffer

      Fresh RNAse is really critical. Otherwise this will result in 10 fold more RNA contaminant than DNA; which implies the nanodrop reading and gel visualized DNA will be 10 - 100 fold different. (from personal experience of 1 prep only)

    1. deep-well plates, require a faster shaking speed for proper aeration

      Deepwell plates (24 well plates with 3ml cultures as well as 96 well with 1 ml) require 800 rpm shakers

      • by Bennett Biodesign lab @ Rice University
    1. we recommend calibrating OD using serial dilution of silica microspheres, which readily produces highly precise calibration (95.5% of teams having residuals less than 1.2-fold), is easily assessed for quality control, and as a side effect also assesses the effective linear range of an instrument.
    1. Bacteria are less likely to develop resistance against a pro-drug as it becomes active only after getting inside the bacteria. The active components formed from the pro-drug are potent and short-lived, thus not giving the bacteria sufficient time to develop resistance.

      Would like to see some evidence for this!

    1. which ends up being much less efficient

      Has this been quantified properly? I see a lot of new methods relying on in-vivo homologous recombination now-a-days - ex: FastCloning: a highly simplified, purification-free, sequence- and ligation-independent PCR cloning method

    1. “death phase,” where at least 99% of the cells in the culture lose viability

      So the 'death' in death phase is only loss of viability?

      I thought the cells lyse and are eaten up by neighbours; while reducing the OD (due to cell lysis)

    1. this system enables longer duration production, and could be readily applied to burdensome or toxic products not readily produced in bacteria
    2. Application of synthetic biology is limited by the capacity of cells to faithfully execute burdensome engineered functions in the face of Darwinian evolution
    1. To add a data mask so you can refer to variables in a data frame as if they are variables in an environment.

      Similar to a with() function?

    1. plasmid-based circuits suffer from multiple limitations: high intercellular variation in gene expression, genetic instability from random partitioning of plasmids during cell division, and plasmid loss in environments for which antibiotic use could disrupt native microbial communities or is economically infeasible
  5. Nov 2019
    1. , science proceeds by the falsification and refinement of hypotheses. Thus, for most papers, the only way is down.

      That one nails it!

    2. despite Blatt’s carefully worded insinuations, PubPeer does not allow “hearsay”, “allegations” or invite “innuendo” (and we aim to act on all reports of such comments)

      Blatt does mention that the pubpeer site moderators are anonyomous in contrast to the journal editors. This somehow reduces their credibility on effective moderation of abusive or trolling comments. This sounds like a recursive argument: A central authority brings credibility but also corruptibility. I can see parallels in the debate about Bitcoin cryptocurrency vs federally backed currency and about the trustworthiness vs corruptibility of a central authority as compared to a distributed crowd authority.

    3. authors, journals and institutions are all unquestionably exposed to conflicts of interest when it comes to correcting problems

      A retraction once published does not reflect well on all of these parties and is clearly a conflict of interest even though they may claim that it is in their benefit. Somehow a pre-publication review is being given more importance than a post-publication review because of this reason.

    1. in much of biology, readers have to trust the authors to describe their experiments accurately, and there are many more opportunities for mistakes and dishonesty

      Good point

    1. alleging their negative appraisals of his work had resulted in a university rescinding a job offer

      Oh, and what does he have to say about the 20 retractions he as so far then?

      I is like a real wrongdoer criticising the police for investing in the first place.

    1. Commenting on a scientific paper, in particular when the comments are not positive, is risky business for academics

      Could someone elaborate on this? Why exactly does negative commenting cause a researcher to be discriminated against?

    1. That means gram-negative bacteria cannot change the BamA protein without losing their ability to infect.

      It 'suggests' that would have been better. There might also be other resistance pathways that might retain infectivity. This will depend on the environment used for the resistance evolution experiment

    1. (a+b+c)^2 - a:b is identical to a + b + c + b:c + a:c

      This example is not clear. I do not understand what a:b means

    1. Ina Schuppe Koistinen, Abhishek Krishnagopal, Sangeetha Kadur, Pooja Gupta etc gave me the inspiration to do what I wanted to do. Along the way I got exposed to more art and science creators like Gemma Anderson, Monica Zoppe, Drew Barry, Ina S. Koistinen, Christian Sardet, Sandra Black Culliton, Amanda Phingbodhipakkiya

      science communication - art + science

    1. we present an overview of our current understanding of these rules for the genetic manipulation of prokaryotic microbes and the available genetic tools to expand our ability to genetically engineer nonmodel systems
    1. s used fluorescein-labelled oligonucleotides as our probe for DNA delivery

      DNA delivery assessment

    2. required removal of salts results in osmotic stress - particularly challenging for a notoriously temperamental marine bacterium like Prochlorococcus

      Electroporation buffers cause osmotic stress and need osmoprotectants like glycerol

    3. the 6-month multi-step procedure is vulnerable to user variability

      The doubling time is 3.3 days!

      • Genetic Manipulation of Prochlorococcus Strain MIT9313: Green Fluorescent Protein Expression from an RSF1010 Plasmid and Tn5 Transposition
    4. This cell is the simplest photosynthetic “machine” designed by nature – an attractive foundation for manipulation
    5. small size (hence high surface/volume ratio), which enhances its ability to compete for limiting nutrients
    6. Such projects are not suitable for graduate students or post-docs because of the high risk involved, nor are they easily funded

      that is wisdom!

    7. genetic transformation protocols requires tedious trial and error, and methods developed for one strain are often unsuccessful in close relatives
    8. To avoid the pursuit of unproductive paths, we report here what has not worked in our hands, as well as our progress developing a method to screen the most efficient electroporation parameters for optimal DNA delivery into Prochlorococcus cells

      negative results

    1. HGT typically adds new catabolic routes to microbial metabolic networks. This increases the chance of new metabolic interactions between bacteria