text:
How to estimate the scientific consensus or not about Hydroxychloroquine?
In several (political) discussions, I have been told that there are around 200 papers stating that the Hydroxychloroquine is successful in treating COVID-19...

Is this statement true?
How can we estimate coldly and reasonably the absence or not of scientific consensus about Hydroxychloroquine regarding COVID-19?

I'm not able to judge: I am not a virologist myself. But I have a modest statistical background that made me have extreme doubts about the behaviour of Dr Raoult: Answers to my statistical question in April 2020 https://stats.stackexchange.com/q/459501/2910 highlight those doubts.
Looking back in time, there are things that does not help the seriousness of RAOULT statements:
During January February and early March 2020;

in those times Dr. Raoult was mocking Coronavirus repeatedly , saying pandemics only exists in video games (I'm gonna a add a link to this one, it's just mind-blowing to see his carelessness)
Dr. Raoult was also joyfully repeating that Dr FAUCI was senile.

But:

there may be personal conflicts between FAUCI and RAOULT
there may be pharmaceutical conflicting interests. That already happened in the past in other economical fields... Yes that can exist sometimes, so that remains possible. In France, the Raoultmania and friends transforms this argument into: "Big Pharma" wants to bring down Dr. Raoult at all costs, he is the best virologist in the world, he is "the only one" real specialist.

So what to say to people saying that there are 200 scientific papers concluding that Hydroxychloroquine is effective: maybe there's a possibility to know how many papers are stating the contrary?
Any pointer is welcome. Even in my family it has sometimes become a political drama. I would like facts, or factual trends, or constructive conclusions based on clearly stated hypothesis.
I don't know where to start and it is important for me. And I clearly don't want to fall in the opinion-based trap.

As it is important for me, I'd really appreciate downvoter(s) to guide me on how to gather more scientific facts about my question, or how to refocus it. Any comment appreciated.

I don't speak for the downvoter(s), but your question (at least as currently written) seems to be off-topic for this site. Most of your post is about politics and the core of your question seems to be how to evaluate whether there is a scientific consensus about this subject. Unfortunately I don't see how that can be answered in a way that depends on facts rather than opinions — this contradicts one of the criteria for good questions mentioned in the [help], see for example [ask]. This is also more of a medical question rather than a biology question.

I think Skeptics.SE cover questions of "how much support is there really for this in the scientific literature".

This question is off-topic in my opinion in that it is not a question about biology or even medicine (that would be "is hydroxychoroquinine effective against covid?") but about reaching decisions and arguing with others. Both of these are in the realms of sociology and psychology. In life we all make decisions on incomplete data. I trust the scientific and medical institutions in advanced Western societies (Britain, the US, W. Europe) and so if they haven't rejected this I trust there is a good reason for it. I don't need to read 200 papers to make my decisions in life. cont.

cont. If you haven't come to the same conclusion of me I might have a low opinion of your decision making, but I need to ask myself why. What social influences have prevented you coming to what I consider the obvious conclusion. I am not going to argue with you because I realize it is a waste of time. Likewise, should you decide that hydroxychloroquine is snake oil, I don't reckon much for your chances of convincing your family unless they regard you as some sort of a guru on the subject.

Hardly, the question that's been asked seems to be entirely about plain fact.

@A.B. I understand your point of view about forwarding to Skeptics. However I doubt I might access the reading span of virologists. I have tried on Reddit but they don't take plain text question/statement on Covid subreddits that I know about.

If you don't have the time or inclination to develop the skills to evaluate scientific papers on your own, you pretty much have to take other peoples' word for it.  Even if you are not knowledgeable in a field, you can evaluate things like experimental design, data analysis, consideration of possible alternative explanations, etc. The infamous Turkish study involving measuring blood oxygenation before and after performing a surgery (with masks on) should certainly provide examples of poor experimental design.

@Armand But you can at least try to use your judgment about whose word you take for it - as the OP did by coming here.  Better to take the word of someone who's studied biology, and how to evaluate papers, than of a random person in a political argument.  (Good point that a lot of the most basic ways of evaluating a paper apply to lots of fields.  As bob1's answer says, one very important one to know in anything medical is sample size.)

Oh, and if the OP (or anyone else) is interested in learning more about why not all published scientific studies should be believed and how to recognise good ones, I recommend a recent book called "Science Fictions" by Stuart Ritchie.  Crammed with information and really entertaining - and unnerving, in places.

Not sure why this is getting upvoted. Whilst interesting, it's clearly offtopic as Tyersome and David have pointed out.

Skeptics.SE has been mentioned; note that there are already several questions there on this topic. This answer might be the most relevant.

Sientific debates are no deifferent than thsoe in real life or politics: there are may be people believing one side or the other, and on some occasions the debate may be distorted by the political and financial considerations involved. The level of the debates is however very different, and the debated points are much finer - I would not be surprized, if Mrs. Fauci and Raoult agree about the positive and negative sides of Hydroxichloriquine a lot more than their supporters/detractors. contd.

cont. It is instructive to read the recent tribune by a group of renowned scientists regarding the need for deeper investigation of the origins of Covid pandemics, to understand how it differs from peedling conspiracy theories: https://science.sciencemag.org/content/372/6543/694.1

Is "how does one assess the reliability of biology papers" really off-topic?  I'd have thought that bob1's answer would be very useful for a lot of other visitors.

@David Does the thoroughness of the answered question change your point of view? Would you have been able to reach such an explanation? I would not have been able to formulate such response. In your comment, to siplify, you say you trust medics etc... The huge problem here is that the Hydroxychloroquine debate has been thrown in the public debate during election campaign in France. And just like in the US with Fox News and Trump, there is a lot of Raoultmania on the right and far right. And that pleases a lot the inner "egomania" of Dr Raoult: it is a choice from him to move the debate there.

@David this is the reason why I asked for a clear, un-opinionated description of how to evaluate scientific consensus (so as to have trust in Science like you do), and how to reach a conclusion based on that. You have to understand that Raoult and friends propaganda says to people "look at all the science that says our treatment works, just look" - the same technique used by Trump during his Ukraine affairs, telling supporters "read the transcript", knowing nobody in the right-wing will read the transcript for real. That's the same technique. And it's not by chance they use the same technique.

@David you have to remember that Trump world-widely promoted Dr Raoult's treatment a few hours after the paper was released. 24h IIRC. I would be surprised if Trump was a daily reader of scientific papers.

This site deals with specific problems in biology. One such problem related to your concern might be "Is Hydroxychloroquine an effective treatment for Covid 19?", although I would think it more appropriate for SE Medical Sciences. But your question is really about the philosophy of science or of life — How do we distinguish between what is true and what is false, as individuals, as scientists — and hence is not on topic here. And of course, human judgement involves a heuristic approach, which doesn't always produce the right answer. There is no perfect approach, but there are sane ones.

@David thanks for your answer. Unless I did not pay enough attention, it is too bad you or someone-else did not ention SE Medical Sciences before. I was touchy about skeptics SE but your suggestion is right on spot. I share your point of view that it would have been much better there. I'd correct you on one point though: my question is about Virology, and how to estimate how/if a consensus is reached in Virology (Dr. Raoult says he is the best virologist in the world). I've suscribed to SE Medical Sciences, and if ever I have topics that are more appropriate there, I'd follow your indication.

The difficulty here is that these sorts of questions are hard to understand for non-scientists and the results difficult to interpret for non-scientists.
This will be long, and I will likely miss things while writing this, so anyone please feel free to weigh in and/or edit if you feel the need.
First some background about treatments and how we (scientists and medics) know they work or don't work:
In general for a drug to be assessed for its efficacy it needs to undergo something known as a clinical trial. These are studies that involve proper experimental design and have at least one testable hypothesis with results that can be interpreted statistically. Proper experimental design for these sorts of things is difficult and aims to ensure that any there are no biases in the data that may invalidate the results!
First off the trial should be controlled in some manner. Control in this context means a comparison group who receive something other than the treatment in question. This might be that the patients receive a different drug (of known efficacy or not) or a placebo. You can even compare different doses of a known efficacious drug (say you know it works a dose X, but you want to see if it works at 10-times that dose). You can also compare things like surgery with no surgery - sometimes by doing mock surgery as a placebo.
The treatment also has to be tested in a randomized manner (assigned to some participants on a random basis), you also need to make sure that neither the participants nor the people giving the drugs know which people are receiving the placebo and which the real drug(s) until after the results are in and have been fully analysed. This is a process known as blinding. There are quite a few different sorts of blinding. The one I described above is called double-blinding.
If you put all these things together you have what is known as a controlled randomized double-blinded study. These are often considered the most effective at determining the efficacy of treatments. Not all trials will meet these conditions - for example it would be very hard to double-blind a surgical trial as it would be hard to blind a surgeon as to whether they have done real surgery or not.
Next, clinical trials should also ideally involve lots of random participants from random populations so as to not introduce bias(es) (for example: don't sample just a few patients from your local hospital when you live in a high-wealth area and assume that your results are able to be generalized to the whole population). This means you should sample young, old, rich, poor, body types etc). There are a few exceptions to this rule - perhaps you want to examine the effect of a particular treatment on obesity (so you need obese people to start with) or perhaps a particular age-group, but that can be part of your experimental design so is less of a problem, but you still need to sample randomly within that group
However,in addition to all of the above, there are a few more conditions that should be met:
The next rule is that you need to sample large numbers of people - often in the several thousands. Smaller sample sizes may have larger (relative) biases (e.g. maybe, just by accident, 50% of the 60 patients in your trial were from a single family with a genetic mutation who all caught the bacterial infection you are studying at a family gathering - which could bias your results towards how that genetic mutation affects your treatment). Another issue is that small samples may not have enough statistical power to show minor effects. Proper experimental design will have determined the statistical power needed and how large the minimum sample size should be before the study is conducted. Large sample sizes also allow you to look at different groups within the study during analysis - perhaps your drug isn't effective in the population as a whole, but it is in those over age 70, or those with kidney disease or a missing left leg (very unlikely - but you wouldn't see this last unless you had a large enough sample size!).
A clinical trial should also be registered with a clinical trial register (e.g. The USA one) with open methodolgy and aims etc. outlined. As I write this, there are 5874 clinical trials on COVID-19 registered on the Clinicaltrials.gov website from all sorts of places around the world and looking at things from known treatments (e.g. remdesivir) to wearable smart devices.
Another requirement is that the results are reported in the literature (we are getting closer to your question here...). If they are a well designed study that meets all the above criteria and show a result of interest to the medical community, then it should have no problem with peer-review (where experts working in the field examine all aspects of the trial before the results get published) and will likely get published in a well established  and respected scientific or medical journal.
Thanks to @BenBolker for the following idea and paper:
To show you just how hard all of this is, there's a review paper in the British Medical Journal (BMJ, one of the top-ranked medical journals) with the title Drug treatments for covid-19: living systematic review and network meta-analysis. Link to article: here. What this paper aims to do is to look at many of the drug treatments for SARS-CoV-2 infection and aggregate data from all the published trials from the start of the pandemic through to February 2021. The abstract provides a summary of the data starting out with inclusion:

196 trials enrolling 76 767 patients were included; 111 (56.6%) trials and 35 098 (45.72%) patients are new from the previous iteration; 113 (57.7%) trials evaluating treatments with at least 100 patients or 20 events met the threshold for inclusion in the analyses.

This means out of the ~200 studies, just over half met the criteria of significance (for this analysis) - they excluded vaccination, nutrition, antibody-based therapies, supportive therapy and traditional therapies that included more than 1 active molecule.
As further evidence of how hard it is:
Figure 1 from the BMJ paper shows the triage process for the articles they looked at. It shows that they started out scanning 31,752 articles on COVID-19 and trimmed that down to 632 randomized trials, which were then examined closer and found that 343 of these weren't actually randomized or were excluded for other methodological problems, leaving 289 trials. These were then pruned to 206 for a bunch of reasons (duplicates, pre-print (so not verified), corrections, retractions etc.) leaving 196. A further 83 were excluded for not meeting criteria on size, lack of data, no outcomes reported or same-drug comparison (not controlled properly). Leaving 113 in total.
So if you take the 632 trials and are left with 113... that's only about 17%: less than 1 in 5 get it right!
Now, this is where it gets murky! What is a "good" journal? Well, that's a tale for another day, but there are many "scientific" journals that are neither scientific nor good. Many of them are listed on Beall's list, which is a list of publishers and journals known or suspected of being "pay for display" - essentially pay them money and they will publish your paper without doing the proper peer-review process, which science uses to determine if a study meets scientific standards and rejects those that don't.
Unfortunately, proper peer-review takes time - the journal gets a paper submitted to them. An editor reads and then rejects or sends out for peer-review. The reviewers then read the paper, write a report suggesting problems, fixes, questions etc - these then get communicated to the editor, who either rejects the paper or sends it back to the authors for amendments (may be needs more experiments, more statistics etc). The authors fix and then re-submit to the editor, who again reads and sees if the review has been addressed. The paper may then be sent out to the reviewers again, rejected (if concerns not addressed) or published. Generally this takes between 3 and 12 months.
With the current pandemic there has been a problem with this system of peer-review. Because of the urgency of the pandemic and the strain on resources, people have been submitting papers to journals for peer-review and posting them on "pre-print" servers (not peer-reviewed), where they are read and used, based on the information presented. Many journals also suspended peer-review because of the need to get information, especially about therapeutics, out to their audiences as quickly as possible. This resulted in some of the checks-and-balances that normally go on in the scientific field to be suspended and papers published that would not normally have passed peer-review.
We are now finally at the point where I can discuss Hydroxychloroquine (HCQ):
Hydroxychloroquine has been around for a long time and touted as a potential therapeutic for a number of diseases. It works well for rheumatoid arthritis, systemic lupus erythrematosis and as an anti-malaria drug. However, it has never been shown to be an antiviral in any form outside of the laboratory.
Initially reports of HCQ as a treatment for COVID came out in May 2020 (e.g. this British Medical Journal paper (an excellent journal). These were small trials which were some times randomized and generally non-blinded (AKA open-label), and showed variable effects. 6 out of 8 papers mentioned in the FDA revocation of emergency use for HCQ letter (see Table 1 on page 5. PDF!) show no effect, while 2 do, with the largest in terms of numbers of people (the BMJ one linked above) showing no effect. The ones that do show an effect are very small sample size
Based on the evidence presented in some of these studies and (I think, can't find publications) some laboratory data indicating that HCQ might be effective against SARS-CoV-2, the FDA issued an emergency use authorization (I also don't know if there was some political interference in this). At the same time the University of Oxford (UK) started recruiting for a large clinical trial of HCQ. This trial is known as the RECOVERY trial and is not just for HCQ, but a bunch of other drugs too. Currently they have recruited nearly 40,000 patients for their trials across multiple countries.
The results from the RECOVERY trial into HCQ were released in June 2020 (this is very very quick for a clinical trial, but then massive numbers of patients) with 11,000 patients tested in a randomized, controlled, double-blinded manner. The results were then published in New England Journal of Medicine (another excellent journal) and showed no effect of HCQ on any of the metrics recorded. Since then other trials, mostly smaller ones (~1000 patients) have been run by a bunch of people, none of which (to my knowledge) have found any effect of HCQ on SARS-CoV-2 infection.
Taken together, but heavily weighted towards the results of the RECOVERY trial, the data indicate that HCQ is not effective at all against SARS-CoV-2.
Edited to add: @Chris has commented with a link to a site that aims to look into the science behind medicine and some of the claims made around therapeutics and make it available for the layman. The link for hydroxychloroquine is here

You are right (as far as I followed this up): There is no proper trial (number of patients, controls etc.) which has found an effect of HCQ. Only the very early, methodically heavily flawed "studies" saw small effects. This should have been a massive warning sign on its own.

Wish I could upvote this twice!  It sounds as if the answer to the "200 papers" thing is that if there really were 200 papers in favour of HCQ, they were rubbish ones.  All scientific papers are not created equal and, sadly, there are a lot of rubbish ones about - just because something is stated in a "published paper" does not by itself mean it's reliable.

https://www.bmj.com/content/370/bmj.m2980 ("Drug treatments for covid-19: living systematic review and network meta-analysis") is a very good reference. Someone who felt like it could build an answer based on that resource ...

@BenBolker thanks. I've edited that in with some explanation about difficulty of doing trials correctly.

To add to your answer: The blog "Science based medicine" has a number of articles on this topic: https://sciencebasedmedicine.org/?s=hydroxychloroquine&category_name=&submit=Search

@Chris thanks for the link, that is a wonderful site, I am sure I will spend many an hour there shaking my head at the lack of science behind so much of the disinformation going around. I'll edit the link into my post.

@bob1 You will need time :-) And they have a lot of good articles on other topics as well.


text:
MCQ - Events in the Mitotic cycle
The following question confused me at first

However, I presumed that it must be in comparison to meiosis. In that case D would be correct.
However, the correct answer is A.
How can this be? I know that in mitosis it is the chromatids that are 'pulled away' to opposite poles. In meiosis, this is whole chromatids but anaphase still occurs.
I suspect I don't understand the question. Where have I gone wrong in my reasoning?

Cell cycle can be divided into two phases:
1. Interphase
2. M-phase(Mitotic phase)
Note: M-phase can also mean Meiotic phase but it is not the full form of the acronym.
So M-phase in mitosis has four phases:

Prophase
Metaphase
Anaphase(your answer)
Telophase

A mitotic cycle:

The rest of the options:
B. Cytokinesis

Cytoplasmic division begins during or after the late stages of nuclear division in mitosis and meiosis.

Your question doesn't seem to consider cytokinesis as a part of M-phase (i.e to be occurring during the late karyokinesis). So it has to be ruled out.(Making some assumptions as this is a key to reaching the single correct answer in MCQs, if not this would have had two right answers.)
C. DNA replication - happens in S-phase of interphase
D. Interphase (certainly not the one)
Source: ncert

source: Stack Exchange

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/

sort: votes


text:
Is every decision we make already "pre-programmed" because of DNA?
DNA has information about our cells and how every cell should act.
Since I am made entirely of cells, including things that make my mind, aren't decisions coded for by DNA by proxy of our cells.
Even asking this question is a decision that has already been made because that's what my DNA told my cells to do?

There are so many other factors, some that we know like epigenetics, upbringing, the environment, and probably others we don't know like how exactly our brain takes a decision. No, I don't think your DNA makes your decisions. But it influences them.

This question appears subjective, but I think can somewhat be answered in an objective framework so long as we avoid "I reckon" answers. We should answer it here rather than flagging as a duplicate of philosophy SE because biology comes at this from a different angle.

There is a misconception of the information coded in DNA here, but to me this seems more like a fundamental question about free will versus determinism.

@arboviral I'm keen to have a question that comes at that debate from a biology PoV where we can have scientific contributions to an answer about what biological stuff contributes to our thoughts and sensation of "free will" (I think Remi.b and I have provided some reasonable answers already). If you have any suggestions on how to shift the focus away from top down arguments, to bottom up ones, please do suggest an edit to the Q!

@James fair enough. I've suggested a slight edit to the title that makes it sound more 'biological'.

Incidentally it's been twenty years since I read it so I can't write an answer based on it from memory, but from what I remember 'The Extended Phenotype' (from back when Dawkins stuck to writing interesting books) essentially takes the opposite view from the existing answers and argues that genes do determine our behaviour. You (OP) might find it an interesting read, assuming it isn't what prompted this question, although it's probably dated a bit. You might want to start with Selfish Gene though - it's essentially a sequel.

Just a detail of semantic for your title; "DNA" is not an explanation (or a hypothesis), it is a molecule. "our decision are dictated by our DNA only" is an explanation (or a hypothesis). Saying "decsions are pre-programmed because of DNA" would be like saying "Paul will be here soon because of car". It does not mean anything. "Paul will be here soon because he took his car" would be correct, as "he took his car" is an explanation (hypothesis) but "car" is not.

"Do we have free will?" It's a big question.
DNA (among other epigenetic factors) code for proteins, so ultimately it determine our cells, which in turn are responsible for our neurology, although how this translates to behavior is variable depending on factors beyond DNA@Remi.b's answer. De facto you're asking about the extent that our brain structure and neural activity determines our conscious stream. This boils down to "Do we have free will?". That question historically was only accessible to philosophers. It is now accessible (but not completely answerable) to biologists, more specifically neuroscientists. It's a great question, but is still open to a lot of subjectivity.
An evolutionary explanation.
Anil Seth, professor of cognitive and computational neuroscience at the Sackler Centre at the University of Sussex, gives a very good answer to the question at 25:44 in this BBC Life Scientific interview.

We are determined to have it in both senses of the word...
Yes, we do have free will because we can behave the way we wish to behave. We cannot decide what to will.

Paraphrasing the guts of the answer: it's very important for the brain to differentiate between internalized experience, and reflex.
Reflex, such as placing your hand on a hot stove, never reach the "conscious stream". These have an obvious correct choice; in this case, removing the hand from a hot stove is clearly the right choice, every time.
Then there is internalized experience. Complex problems have many potential losses and gains. To cope with this, the brain needs to internalize, reflect, and is taking note and making a plan; the sensation of free will. By taking note of that situation within it's context and the plan, we can perhaps change our actions the next time we encounter a similar event so that we can optimize our choices to attempt to cause the least damage to ourselves and/or maximize the benefit.
How is learning achieved.
We have established that there is a need for new memories to form in order to solve complex problems. Long term memories are the result of new physical synaptic connections in the brain. This connection endures whether it’s being used or not.
Psychologists put these into two broad types are two kinds, implicit (akin to reflex; how to read, how to play your favorite song on an instrument etc.) and explicit (the things we are consciously aware of). Explicit memory comes in two forms: episodic and semantic (Tulving, 1972). (i) Episodic memory includes experience. For example, that time you planted some seeds and a potato grew. (ii) Semantic memory is abstract to your own experience. Something more like "Primordial potatoes originated in southern Peru".

To bring this back to the original question "Is every decision we make already pre-programmed because of DNA?" It's long winded. Our choices are built upon the results of our past choices in a given environment. We are able to make these choices, to an extent depending also on other variables, because of the products and machinery encoded in our DNA.
The philosophers answer
If this answer is a bit scary or makes your choices seem futile, you can simply sit around and do nothing instead of doing whatever you normally would do; it's your choice.
See a similar question answered from a different perspective over at Philosophy.SE.

Your answer is drawn from philosophy and not from science. If this is what the OP what expecting, then the question is off-topic on Biology.SE.

I'm presenting the (brief) opinion of a scientific expert in the field. This is not philosophy, but you're right it's not science either. There is currently no empirically falsifiable hypothesis surrounding free will (even the same environment in controlled twin studies will lead to different experiences for either twin; it's not good enough). Presented in this answer are good reasons why the sensation of choice should exist despite a rigid framework of genetics and environment that determine our phenotypes. I've removed some fluffy wording, but there is still room for improvement!

Is every decision we make already pre-programmed because of DNA?

No! An obvious way to realize this is to compare identical twins. While two randomly chosen twins ressemble each other (in terms of appearance but also in terms of behaviour) more than two randomly sampled individuals in the population, it is still true that they are not exactly identical. So something else than DNA must affect behaviour. What is it?
Phenotypic trait
Let's first define what a phenotypic trait is. Broadly speaking, the phenotype is the consequence of the genotype on the world. Loosely speaking, a phenotypic trait is any trait that an individual is made of! This includes the colour of the hair, the behaviour, the nature of emotions and the decisions. Decisions are nothing but the phenotype of a person.
Phenotypic variance
For any trait, you may (or may not) see variation for this specific trait in a population. You can therefore calculate a phenotypic variance for a specific trait and then wonder what is causing this variance. Is it only DNA or is there something else in play? Let's call the phenotypic variance for a given trait $V_P$
What is causing phenotypic variance
Why would a population display any phenotypic variance? Why wouldn't we just look exactly asame? What explain these differences?
There are two main sources of variance that are underlying this phenotypic variance. The first one is the genetic variance and the second one is the environmental variance. We will call the genetic variance $V_G$ and the environment variance $V_E$.
To appreciate the role of genetic variance $V_G$, consider comparing difference in height among countries as an example. To appreciate the role of environmental variance $V_E$, consider comparing the body shape of people eating at McDonald and those that don't.
So does $V_P=V_G+V_E$?
Is there something else than environmental and genetic variance that explains the phenotypic variance? The answer is yes. Therefore $V_P>V_G+V_E$. So what is this something that causes this inequality?
Gene effects and environmental effects covariance
Well, first there is a potential non-zero covariance between the environment and the genes. Let's call it $COV(E,G)$. For example, thinking of animals that compete for territory, individuals that have alleles (an allele is the variant of a gene) that make them bigger might be better competitor and have access to bigger territory and therefore to more food which in turn will make them bigger. In such case, there is a positive covariance (or positive correlation) between gene effects and environemtnal effects.
Developmental noise
The developmental process can be quite noisy. An obvious way to appreciate its noisiness is to acknowledge differences between right and left side of people's face. Such noise bring some variance in phenotypic trait in the popualtion. let's cal the contribution of this variance $V_{DN}$. Of course, the amount of developmental noise might depends upon the environment or the genes so that we should also consider covariances.
Epigenetics
Epigenetics also yield to some variance and epigenetic effects may well covariate with gene effects, environmental effects and the effect of developmental noise, so again we should consider all covariances. Let's call the variance due to epigenetic effects $V_{I}$.
Putting all these variances together
So, if $V_P=V_G+V_E$ is inaccurate, $V_P = V_G + V_E + V_I + V_{DN} + COV(V_G, V_E) + COV(V_G, V_I) + COV(V_G, V_{DN}) + COV(V_E, V_I) + COV(V_E, V_{DN}) + COV(V_I, V_{DN})$ would be a bit more correct.
Coming back to the question
So, genes do explain part of the variance in behaviour and appearances in human (or any other living being) populations. But it is by far, not the whole thing! The things one experiences through its life typically will greatly affect its future decisions.
Source for a more complete answer
If you are looking for definitions that are a bit more rigorous than those I have been using here, or for a more complete explanation, then you should definitely have a look at my answer at the post Why is a heritability coefficient not an index of “how genetic” something is?. It will also teach you the concept of heritability.

Please leave a comment when down voting (2 down votes for the moment)!

I like this as a complete answer for "Are we more than our genes?". You clearly show that there are a lot of variations in our traits that cannot simply be explained by our genetics. However the answer is missing a step between "our genes don't determine our traits" and "our genes don't determine our choices". I'm not exactly sure what that step looks like, but I'm sure it exists!

By the way, I'm not one of the down voters (just an onlooker), and whilst hit and run down voting is annoying, there is and should not be an obligation to explain down votes. That's a discussion for somewhere else perhaps!

A behaviour is a phenotypic trait. Any choice is part of our phenotypic trait. There is no step missing.

I agree with you concerning down votes. After two down votes I ought to assume that something must be wrong in my answer but don't know what.

My only suggestion would be a section trying to define choice as a behavior, and behavior as a phenotype (which are not necessarily dependent on DNA). However, using general rules about phenotype variance independent of DNA to explain the differences in sensation of how two people take the red pill, or the blue pill isn't an entirely satisfying answer. In my answer I discuss what possible benefit the behavior of choice might have in terms of survival, which is more superficial, but satisfying!

Thanks. I extended my definition of phenotype to clarify that behaviour and choices are part of the phenotype.

As Remi already explained, there can be phenotypic variations even if the genotype is the same. This is applicable in a broad sense. I'll focus on your query on decision making.
DNA does encode the developmental programmes in the body (including the brain). Because of conserved developmental programmes, we do have some very basic instincts and reflexes that are usually common between different people (as infants and to some extent, as grown ups too).
However, while the gross developmental programme of the brain is conserved (brain organization etc), memories and other learned preferences arise because of experience. At the cellular scale, neurons establish synapses with multiple other neurons. Experiences either strengthen or weaken the synapse. These experiences are based on how often (and in what way) these neural connections are used, which is in turn based on interactions with the external world. The DNA does have the information to allow the cell to carry out the processes that can strengthen or weaken a synapse but it does not have the prior information of which synapse to strengthen (this is somewhat grossly analogous to body-building, just that you are not always consciously aware of which neural circuits you are training).
Apart from that, there are several cellular processes that are inherently stochastic in nature. The effect of stochasticity dominates when the number of the participating entities in the system is small (such as a few neurons deciding which other neuron to interact with). In such conditions, deterministic models cannot explain the outcome. The stochasticity is also the source of the gene expression noise. When we say that stochastic effects dominate, it means that the system dynamics are governed by probabilities and not fixed deterministic rates.

So the bottomline is:
Decisions are not pre-coded in the DNA, but the ability to gather information and make decisions, is.
So it all depends on what information you gather.

that would be ridiculous. though the situations that we encounter may be quite similar to those for others of the past, we must decide anew what to do in each situation. it is not written in our dna what will happen.

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/


text:
T cell sensitivity and persistence to specific bacterial proteins
Currently, the standard tests for Lyme Disease measure antibody production after exposure to a bacteria, Borrelia burgdorferi. Often, the tests are performed too soon after infection, before antibodies can be produced.  Also, infected patients experiencing immune suppression may not have detectable levels of the antibodies to the antigen. In both cases, test results are often false negative.
A new test for Lyme Disease has been developed, ISPOT Lyme by Pharma Labs, which focuses on T-cell activity instead of antibody production. Modeled after the ELISPOT test for TB, it measures interferon gamma (IFN-γ) secreted by T cells in response to stimulation by the B. burgdorferi antigen proteins -- DbpA, OspC, p100, and VlsE-1. After isolating and culturing lymphocytes from a patient's blood sample, they expose the cultured lymphocytes to the B. burgdorferi antigens. If the lymphocytes 'recognize' the antigen, due to previous exposure, they secrete IFN-y which reacts with a blue-colored dye visible in the culture.
Question: Can T-Cell exhaustion affect the usefulness of a serological assay which measures T-cell sensitivity to specific antigens?

It is called ISPOT for Lyme Disease, Pharmasan Labs.  Unfortunately, the only acess I have to information about the test is promotional literature.  However, it is fast being touted among patients in the Lyme community as THE answer to diagnostic testing because it focuses on T cell sensitivity instead of antibody production.

If at all still interested:  The iSpot Lyme test uses the ELISPOT technique to count B. burgdorferi-sensitized T cells by capturing IFN-γ secreted by these T cells. More specifically, when IFN-γ is released a spot of insoluble precipitate is formed at the site of the reaction. Evaluating the number of spot forming units (SFUs) provides a measurement of B. burgdorferi sensitive effector/memory T cells in the peripheral blood. The SFU count correlates to a patients T cell reaction to B. burgdorferi.  That's all I've got.


text:
What is the difference between a signal peptide and a transit peptide?
From what I know, the two names are used interchangeably and I haven't found any resource which says otherwise either. Is there at all any difference, is there a transit peptide that is not a signal peptide or vice versa?

Signal peptides are typically located at the N terminus of a protein. The signal peptides are processed by the translocon machinery and are cleaved off after sorting through the membranes of organelles in the secretory system:

endoplasmic reticulum
Golgi apparatus
ER-Golgi transition vesicles
plasma membrane
lysosomes

Transit peptides target the protein to other subcellular organelles such as (from UniProt):

Mitochondrion
Apicoplast
Chromoplast
Chloroplast
Cyanelle
Thylakoid
Amyloplast
Peroxisome
Glyoxysome
Hydrogenosome

N-terminal transit peptides are quite rare. C-terminal transit peptide motifs are much more common. UniProt holds transit peptides as a discrete controlled vocabulary, separate from signal peptides.

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/


text:
Can a chicken really be hatched outside of the egg?
This YouTube video (screenshots attached) claims to show Japanese schoolchildren breaking an egg into a kind of clingfilm "hammock in a cup", and then growing and hatching a chick from it in an incubator.
Is this really real?
My first immediate thought is, "If this can happen, why don't the eggs in my cupboard at home sometimes hatch? Why do I never see an embryo in my frying pan?"
Obviously the egg has to be fertilised, but depending upon where you get your eggs (like an "organic home farm" or something) this might happen.
If it's more a matter of temperature, how warm do the eggs have to be? For how long? (ie, Could a warm kitchen cupboard in a hot summer do it?)
What other biological requirements are there to make this work?

It is perfectly clear what the question is, and it is not a subjective answer. I'm not sure why this question was flagged for closure. @WYSIWYG's answer covers it comprehensively.

The eggs have to be kept warm for the embryo to develop. They're removed from the nesting boxes as soon as they're laid so the embryo never has a chance to develop.

Yes it is real, in the sense that this protocol has been through a peer reviewed journal.
Note that the embryo is developing outside the shell, not outside the egg. It is the fertilized egg that develops into the embryo. The shell only provides protection and allows exchange of gases. You can replace the shell with any other material that does the same job. Embryos of non-placental animals can grow in a petridish as well. Someone seems to have done this back in the 1980s (Scadding, 1981).
You can see a video along with the detailed protocol of this process in this article published in the Journal of Visual Experimentation.

Why do I never see an embryo in my frying pan?

Because it has probably become an omelette.

how warm do the eggs have to be?

37-39oC is the ideal temperature and usually hen eggs hatch in 21 days (common poultry facts). However, the incubation time can depend on other factors (including temperature) such as humidity and air composition.

At first glance, this seems like it might be a good way to monitor embryonic development in the chicken, since you could see the whole process in real time. But you point out that this was probably done in the 80s. Any thought on why it never caught on?

@user137 I don't have a great knowledge of history of embryology but as far as I know chick embryo was a model system for embryology since long ago (and for quite some time). So I guess people would have actually used this technique. Possibly people started working on other model organisms later on.


text:
What is the last heavy atom of an amino acid?
I'm a electrical engineer and I'm learning about bioinformatics. I was reading this paper that uses the last heavy atom to search for active sites of a protein but what would be a heavy atom? Is it all atoms but hydrogen? Atoms heavier than carbon? And how do I know which is the last heavy atom?
The article: http://bioinformatics.oxfordjournals.org/content/early/2014/11/08/bioinformatics.btu746.full.pdf+html
It talks about the last heavy atom under Materials and Methods 2.1.1 Individual Representation and Population Initialization

Your description is not quite clear. Can you please give the complete reference for the article you're reading, and also the precise quote?

http://bioinformatics.oxfordjournals.org/content/early/2014/11/08/bioinformatics.btu746.full.pdf+html

It's under materials and methods on 2.1.1 Individual representation and population initialization

I haven't heard of this concept before, but it looks like the LHA is a reference atom at the "end" of the amino acid side chain. The precise definition appears to be empirical / heuristic, see http://www.cbi.cnptia.embrapa.br/SMS/STINGm/help/lha.html

As mentioned in the comments by Roland, this term is not common and is first used by the authors of the mentioned paper (also the package mentioned by Roland in comments - STING).
From this link you can find the definition of the Last Heavy Atom which is possibly the most distal non-hydrogen (N, C, O, S) atom in the amino-acid side chain.
$$\begin{array}{|c|c|c|c|}
\hline
Ala\ :\ C_\beta & Asp\ :\ O_{\delta^2}  &Trp\ :\ C_{\eta^2}  &Asn\ :\ N_{\delta^2} \\
\hline
Lys\ :\ N_\zeta & Glu\ :\ O_{\epsilon^2}  & Ser\ :\ O_\gamma  & Gln\ :\ N_{\epsilon^2} \\
\hline
Cys\ :\ S_\gamma  & His\ :\ N_{\epsilon^2}  & Tyr\ :\ O_\eta  & Val\ :\ C_{\gamma^2} \\
\hline
Gly\ :\ C_\alpha  & Leu\ :\ C_{\delta^2}  & Met\ :\ C_\epsilon  & Ile\ :\ C_{\delta^1} \\
\hline
Arg\ :\ N_{\eta^2} & Phe\ :\ C_\zeta  & Pro\ :\ C_\delta  & Thr\ :\ C_{\gamma^2} \\
\hline
\end{array}$$
They have mentioned in the same link that:

If in any of the PDB files (to be analyzed by the BLUE STAR STING components) that specific atom (LHA) is missing in the record, then our algorithms will search for the next closer atom in the side chain that would be considered as the LHA.

The exact location of some of the abovementioned atoms.
Some of the locations might be confusing. So I am just indicating what these are, for a few the amino acids (especially for the branched and cyclic side chains). [Images reproduced from here.]
Arginine

The terminal nitrogens $\eta^1$ and $\eta^2$ are symmetric and the atom that is actually (stereochemically) the most distal is considered the LHA, as inferred from the protein structure. The second choice, obviously is the $\eta^1$-Nitrogen.
Aspartic acid

The two terminal oxygens ($\delta^1$ and $\delta^2$) in the ionized form are equivalent (also otherwise because of resonance). The actual distal atom would be labelled as $\delta^2$
you can extrapolate the same for Glutamic acid
Histidine

$\epsilon^2$ refers to the pyrollic nitogen. .
Leucine

The last carbons ($\delta^1$ and $\delta^2$) are equivalent and the choice is based on the actual distance. Extrapolate for valine
Phenylalanine

$\zeta$ refers to the carbon in the para-position of the benzene ring. For tyrosine the LHA is the oxygen of the para-OH in the benzene ring.
Tryptophan

Proline

For Aspargine and Glutamine the LHA is the amide nitrogen of the side chain.

From a search of Web of Science, it appears that LHA is a term that has been coined by informaticians and is not something that is used in Biochemistry or Organic Chemistry. There are only three articles that are under the topic "Last Heavy Atom," and all three are Informatics Journals. The abstract of this article gives a decent "definition" of the term. http://link.springer.com/article/10.1186/1758-2946-1-13

@AMR Yes it is not a standard term. There are quite some articles that use this term but I guess they are the ones using the abovementioned protein structural biochemistry package.

Seems a bit weird for the cyclic sidechains (except proline), given that they can rotate around the Calpha-Cbeta bond...


text:
Why does sequence of amino acids presented on the Catalytic Site Atlas from a given protein differs from the sequence on the RSCB Protein Data Bank
I wanted to compare the amino acid sequence of enzymes for this project I'm working on and need to compare them at their catalytic site. For that, I went to the Catalitic Site Atlas to get the information on the catalytic site, but since they don't offer an easy way for me to download the structure data programmatically I downloaded it from the RSCB PDB by downloading the fasta sequence. When checking for the catalytic sites it wasn't matching what the CSA was telling me and that's when I realized that they are different files. Take for example the 3nos, the CSA presents the following sequence:
MGNLKS...
While the PDB presents the following sequence:
PKFPRV...
Why aren't they the same sequence if it's the same protein?
Sorry if it's a noob question, I'm not a biologist, just a computer scientist who happens to like bioinformatics.
Important info:
The CSA data comes from here while the PDB data comes from here

Please [edit] your question and give us the exact links you used to download. The simplest explanation is that you are not actually looking at the same protein, but we can't be sure unless you show exactly what you are comparing. For instance, your RCSB link shows two sequences but no information about what species they are from, what isoform, nor whether they're the entire protein. In fact, they look like protein fragments (most proteins start with an M). My guess is that you are looking at the entire sequence in one site, and a subsequence in the other but I can't be sure.

There you go, sorry about that

Crystallography results (pdb files) almost always contain a truncated sequence.
Both ends of a protein are often flexible (even in a crystal) and don't result in enough data for a good fit. The corresponding residues are removed from the model and the sequence, and you're left with only the residues that show a defined electron density.

One sequence is partly contained in the other (highlighted).
So the CSA sequence is (FASTA format, truncated):
>sp|P29474|NOS3_HUMAN Nitric oxide synthase, endothelial OS=Homo sapiens GN=NOS3 PE=1 SV=3
 MGNLKSVAQEPGPPCGLGLGLGLGLCGKQGPATPAPEPSRAPASLLPPAPEHSPPSSPLT
 QPPEGPKFPRVKNWEVGSITYDTLSAQAQQDGPCTPRRCLGSLVFPRKLQGRPSPGPPAP
 EQLLSQARDFINQYYSSIKRSGSQAHEQRLQEVEAEVAATGTYQLRESELVFGAKQAWRN...
taken from http://www.uniprot.org/uniprot/P29474 for convenience.
While the PDB one is :
>3NOS:A|PDBID|CHAIN|SEQUENCE
PKFPRVKNWEVGSITYDTLSAQAQQDGPCTPRRCLGSLVFPRKLQGRPSPGPPAPEQLLSQARDFINQYYSSIKRSGSQA
HEQRLQEVEAEVAATGTYQLRESELVFGAKQAWRNAPRCVGRIQWGKLQVFDARDCRSAQEMFTYICNHIKYATNRGNLR
SAITVFPQRCPGRGDFRIWNSQLVRYAGYRQQDGSVRGDPANVEITELCIQHGWTPGNGRFDVLPLLLQAPDEPPELFLL...
The Uniprot entry mentions 3 different isoforms due to alternative splicing, so perhaps that is what is going on here. Here is the output from a sequence alignment (using https://www.ebi.ac.uk/Tools/psa/emboss_matcher/):

#=======================================
#
# Aligned_sequences: 2
# 1: NOS3_HUMAN
# 2: SEQUENCE
# Matrix: EBLOSUM62
# Gap_penalty: 14\
# Extend_penalty: 4
#
# Length: 240
# Identity:     240/240 (100.0%)
# Similarity:   240/240 (100.0%)
# Gaps:           0/240 ( 0.0%)
# Score: 1294
#
#
#=======================================

NOS3_HUMAN        66 PKFPRVKNWEVGSITYDTLSAQAQQDGPCTPRRCLGSLVFPRKLQGRPSP    115
                     ||||||||||||||||||||||||||||||||||||||||||||||||||
SEQUENCE           1 PKFPRVKNWEVGSITYDTLSAQAQQDGPCTPRRCLGSLVFPRKLQGRPSP     50

NOS3_HUMAN       116 GPPAPEQLLSQARDFINQYYSSIKRSGSQAHEQRLQEVEAEVAATGTYQL    165
                     ||||||||||||||||||||||||||||||||||||||||||||||||||
SEQUENCE          51 GPPAPEQLLSQARDFINQYYSSIKRSGSQAHEQRLQEVEAEVAATGTYQL    100

NOS3_HUMAN       166 RESELVFGAKQAWRNAPRCVGRIQWGKLQVFDARDCRSAQEMFTYICNHI    215
                     ||||||||||||||||||||||||||||||||||||||||||||||||||
SEQUENCE         101 RESELVFGAKQAWRNAPRCVGRIQWGKLQVFDARDCRSAQEMFTYICNHI    150

NOS3_HUMAN       216 KYATNRGNLRSAITVFPQRCPGRGDFRIWNSQLVRYAGYRQQDGSVRGDP    265
                     ||||||||||||||||||||||||||||||||||||||||||||||||||
SEQUENCE         151 KYATNRGNLRSAITVFPQRCPGRGDFRIWNSQLVRYAGYRQQDGSVRGDP    200

NOS3_HUMAN       266 ANVEITELCIQHGWTPGNGRFDVLPLLLQAPDEPPELFLL    305
                     ||||||||||||||||||||||||||||||||||||||||
SEQUENCE         201 ANVEITELCIQHGWTPGNGRFDVLPLLLQAPDEPPELFLL    240

This answer is correct, I just wanted to add that the correct sequence numbering is preserved in the PDB file in the DBREF record (which you can see by opening the PDB in a text editor):
DBREF  3NOS A   66   492  UNP    P29474   NOS3_HUMAN      66    492
In plain English, the sequence presented in this file (3NOS chain A) corresponds to residues 66 - 492 of the associated UniProt (UNP) entry (accession: P29474).


text:
Could we have endless pleasure?
Are there any studies that point out that we could have a device in the future  or drug that could give us endless amount of pleasure by stimulating or blocking processes in the brain or nerve system?
Drugs and alcohol end up saturating receptors in the brain. Is it known inside out how this mechanism of rewards / saturation / abstinence work in the brain and how it relates to consciousness?
It is well known that you cannot have the same amount of pleasure by repeating the same action over and over again but is it truly known how that works? Would it be possible to reset the receptors in the brain to accomplish this?

Biological receptors will saturate after some time. So my guess is it will not be possible (unless some mutant). However, at the end it will become philosophical question about what do you call "pleasure". After experiencing constant "pleasure", you might feel it as normal.

@Dexter are there any serious studies getting into detail? Would it be possible to desaturate the receptors or to block the pain signals sent from the body? Are there any theoretical potential possibilities?

I have little knowledge of neurobiology but I can point out to some similar results in the cell biology. There are constitutively activated GPCRs which always keep signal ON. So theoretically it is possible but concept of "pain" or "pleasure" is multidimentional and their mechanism is complex and not as simple as activation and deactivation. There are some medical conditions where person do not feel any physical pain.

Welcome to Biology.SE! We encourage you to do some research on your own and ask questions informed by what you have already learned. ——— Please also take the time to go through the [tour] and then the help pages starting with [Ask] questions effectively on this site. Thanks!

Of course.
There is a famous set of experiments (Milner & Olds) in biology that basically started modern behavioral research in which a wire was inserted in to a rats brain allowing for direct electrical stimulation of the pleasure center. as long as the current continued the rats experienced extremely high levels of pleasure. To the point they were unwilling to engage in any voluntary behavior, including seeking food and water, even when right next to them if it would interrupt the pleasure. You could keep stimulating the pleasure center until the rats died of thirst.

As long as the experiment is legit and there were no flaws in it this is valid answer. Deep Brain Stimulation could potentially create a "miracle drug".

I think that if you have endless pleasure (with marijuana for example I've read this here) you will not know you have pleasure so it won't exist anymore because you do not know the difference. So could be but you do not realize so is it still pleasure then? Maybe this answer is more philosophical then scientific.

Funny I was told that in the philosophy SE. https://philosophy.stackexchange.com/questions/65609/authors-on-consciousness-and-its-relation-with-suffering What makes you not have the same amount of pleasure with the same thing over and over again? Is that known from a neuroscientific point of view or it is all theoretical

@PbxMan My answer already touches on that, but in general, if you have more questions you should ask them as individual, researched questions, and not ask more questions in comments. You've already edited your answer to include a lot more than it originally did.

@BryanKrause it's just the same question. I added a bit to clarify that it's not a simple question. I'm expecting somebody to post a couple of links saying "if we could do X.... yes or not"."or we don't know how conspicuousness works  yet..." If you feel there is a better formula to ask what i mean please let me know. I'll close the post.

What we call pleasure is effectively the way that we have evolved brains that learn to do what promotes survival and reproduction. Animals get pleasure when we do things that contribute to our survival and reproduction, like eating certain foods or mating; this makes animals (including humans) tend to repeat the behaviors that led to those rewards (of course, just because something is pleasurable doesn't mean it evolved to be that way for the same reasons as other attributes).
We already have ways to "create" pleasure: to do so, you activate the brain receptors artificially that normally are used to inform the rest of the brain that you just did something "good": heroin works great. So do amphetamines, cocaine, MDMA, etc: drugs of abuse. That's why they are drugs of abuse: they hijack the brain's reward system to make taking the drug pleasurable and therefore encourage future behavior to achieve that pleasure.
In animal models, we can also be more direct and use electrical stimulation in the brain to do the same thing: stimulate in the medial forebrain bundle and animals will learn to do whatever led to the stimulation (German & Bowden 1974), even to the point that the reward is saturated (Waraczynski et al 1987) and to the exclusion of other normally pleasurable activities: for example, water-deprived rats will lever-press instead of drinking water (Morgan & Mogenson 1966).
There might be usefulness of these approaches in treating certain types of depression, but otherwise "endless pleasure" seems to not be all that pleasurable due to adaptation and because pleasurable stimulation is relative.
Summary
We can already artificially stimulate the areas of the brain involved in "pleasure"; the result is not great in the long term.

German, D. C., & Bowden, D. M. (1974). Catecholamine systems as the neural substrate for intracranial self-stimulation: A hypothesis. Brain research, 73(3), 381-419.
Morgan, C. W., & Mogenson, G. J. (1966). Preference of water-deprived rats for stimulation of the lateral hypothalamus rather than water. Psychonomic Science, 6(7), 337-338.
Waraczynski, M., Stellar, J. R., & Gallistel, C. R. (1987). Reward saturation in medial forebrain bundle self-stimulation. Physiology & behavior, 41(6), 585-593.

With drugs and alcohol receptors get saturated. The pleasure is temporary not permanent.

@PbxMan Right. Pleasure is "change in reward level"; so, to get more pleasure you have to get more reward. Drugs and electrical stimulation can go all the way to the brain's maximum representation of reward. At that point, there can be no change in reward, so, effectively, no pleasure. Waraczynski is an example.

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/


text:
Regarding hydrolysis of ATP in ABC transporter
So, I was going through this lecture about ABC transporter and one point about it confused me. ABC transporter is not the same as an ATPase but let's take an example of Cystic Fibrosis Transmembrane Regulator. In it 2 molecules of ATP bind with the channel and then they undergo hydrolysis in order for Chloride ion movement to occur. So,if hydrolysis is occurring when ATP was bound to the channel then shouldn't it also function as an ATPase or is it so that it is binding and the channel isn't doing the function of hydrolysis, some other molecule is and it is just using that energy.

"ABC transporter is not an ATPase" - according to whom?

They told me that an ABC transporter is not the same thing as an ATPase

Can you provide a quote? "ABC transporter is not the same thing as an ATPase" is true just like "an automobile is not the same thing as a vehicle" is true. "ABC transporter is not an ATPase" is false in general, though may be true for a specific ABC family member.

See on the topmost of lecture where they write what topic they are teaching, they wrote that ABC transporters are not ATPases but the teacher that was doing lecture said that an ABC transporter is not the same thing as an ATPase. Well by the way can you tell me the difference between the two statements as they seem kinda same to me.

Also, should I edit the question's statement to make it better

@Bryan Krause, I have edited the question so that it'll be more meaningful. But can you please explain that why despite of the fact that hydrolysis is occurring in the channel, it is not the same as an ATPase. Also, why one shouldn't say directly that it is not an ATPase and use not the same thing as ATPase.

I'm guessing your instructor is referring to a family of ATPases rather than functional ATPase activity. But without some sort of quote or actual evidence I'm always hesitant to provide guidance that can mislead a student when there is confusion between what an instructor says and what a student hears.

@Bryan Krause, yes you are right. The teacher was talking about pumps, Na-K ATPase pump to be specific. But as far as evidence goes, I gave you exactly what teacher had said and I'm confident coz I even used subtitles for that video. The teacher had said what you are quoting but I'm confused that despite of the fact that ATP hydrolysis is occurring, why we cannot refer it to as an ATPase.


text:
Is the microscope that gives these images considered professional?
I bought a digital microscope from Dinolite, model AM73915MZT, The use of the microscope is for industries like textiles and printing and graphics and for Ophthalmology / Iridology and Pathology [And as it says on the website that the manufacturer of this microscope is suitable for another wide range of applications].
As shown on the manufacturer's website here
The camera has a resolution of 5 Megapixel (2592x1944), and the sensor is of the CMOS type, with white LED lighting, including Polarizer.
The microscope costs $1469 before VAT and ancillary aids. From what I understand it is the best and most advanced model of this company.
I took some pictures with him, and at 220x magnification I can't get a sharp enough picture.
Attached an image of the calibration target provided by the company along with the microscope.
Image at a magnification of 220 - 10 barcodes

Image at magnification of 50 - 10 barcodes [marked with a red line]

You can see that the edges of the barcodes at magnification 220 times are not sharp compared to the edges at magnification 50 times.
Does this mean that the microscope is unprofessional or damaged and I need to replace it?
Is it related to Spherical aberration?
EDIT:

Both photos were taken with the microscope standing in the best stand of the company, model RK-10A.
If I rotate the adjustment knob slightly to
the right or left, the image only becomes more blurred, which means
that the position in the image is the maximum sharpness.
And for that I wonder if a microscope that this is its maximum sharpness - is considered professional.

EDIT 2:
Attached image of a scratch:
51x

228x

You can see that the 51x image is much sharper and crispier compared to the 228x image, does that mean that the microscope is neither high quality nor professional?
Razor
50x

229x

What microscope is "good" depends entirely on the application. "Professional" for what purpose? I don't think this site wants to get in to product reviews; these are typically off-topic across the whole SE network with a couple rare exceptions.

When I buy a camera I can see reviews on whether it is considered professional and whether it produces sharp and beautiful images, no matter what purpose I buy the camera for, is there no definition in the microscope for professional and good only in relation to the purpose?

For cameras "professional" also depends on purpose. This site is not for product reviews, for cameras nor for microscopes.

But as you stated, it's for textiles and other things unrelated to biology. Just because you intend to use it for biology doesn't make the question as written on-topic.

Professional is a marketing term. Equipment is not professional. People are. There are some instances where the stuff hobbiests use and make is more meticulous than that of paid professionals, because they can't afford to sit there and obsess. Just consider whether it's good enough and reliable enough for what you need it for.

Welcome to the site. For a good answer to this question, you need to provide some specifications on the lenses (type [e.g. plan, apo], f., NA.), camera (MP, CCD etc, plus settings [exposure, gain...], separate camera attachment or eyepiece?), microscope (compound, stereo, inverted, etc), and illumination type. Microscopes vary widely in quality and use-case and are not single instruments. Generally you need to pay $$$ for a good one. I routinely use microscopes with lenses that cost in the $4000 range for a single lens, let alone the rest of the 'scope.

@bob1 I added the details you mentioned, anything else?

Are you certain you have a blurry image of sharp barcodes and not a sharp image of blurry barcodes?

@timeskull What do you mean sharp image of blurry barcodes? If you look at the pixels of the image [for example at an 800% zoom in each image viewer] you will see that the blur structure is suitable for lack of focus - lens blur - and not for smeared ink and so on.

I don't know what technology is used to print the barcodes so I don't know what the edges will look like at high magnification. While I would expect them to be fuzzy, that's not necessarily the case. By my estimation the pixels in the barcodes of your top image are ~5.2 microns. Normal printers / normal paper cannot produce such small features.

@timeskull What do you think I need to photograph to be sure that if there is blurring it is because of the microscope and not from the observed object? By the way you can also see that the blur in all the barcodes is exactly the same, and as we would expect a blur caused by a lens.

you could just put a scratch in a glass slide and image that. If the edges of the scratch look sharp, then the calibration barcodes are blurry in reality. Otherwise, the optics of your microscope are the source of the blurriness.

@timeskull You can also look at the edge of a razor blade. Or a knife has been sharpened and honed by hand on a stone.

Basically you have bought a basic microscope that is not very good, with probably poor quality lenses and low manufacturing quality - the fact that they don't mention the lens manufacturer is a sign that has cheaper lens(es). A lack of reviews on microscopy sites also indicates that it is not well known. It may be suitable for basic hobbyist use-cases, and depending on what you want to do with it, it may suit you. Despite the blurb on the sales pages, no qualified lab would ever use something like this for pathology or any serious purpose; this is more of a toy than a microscope. Celestron has their "Handheld Digital Pro Microscope" that's very similar in specs to yours, but retails for about US$ 150 - just for some comparison from a manufacturer that has a good reputation for imaging equipment (telescopes in their case).
I don't think that it is broken, just that you have reached the limits of its magnification capability and if you were able to move it slightly closer or further away from the calibration you would get this in-focus. That it is out of focus indicates either that the stand is off by a bit (you definitely need a stand for that sort of magnification), or that the manufacturing of the microscope is slightly out. At 220x the engineering specs need to be pretty tight to get consistent focus. You won't get that sort of tolerance on a cheaper 'scope.
This is definitely not spherical aberration, as that would manifest as distortion of the image at the edges - a bit like a fish-eye effect. There will be some aberration in the lens (almost impossible to make one without), but this is probably corrected by a combination of software (like in your phone camera) and cropping of the image to only the centre of the image.
As you have brought it recently I would reach out to the supplier and see if you can get a replacement or a return/refund. If you have brought this for business use, get the company to fork out for a decent microscope brand - not only will they be more robust, they will give much better images and come with good technical support.
Good lenses and microscopes are very expensive and you only consistently get good lenses from well known manufacturers (Zeiss, Olympus, Nikon, Leica are the big names). There are some cheaper brands (e.g. Konus, Celestron [these two mostly known for telescopes], Saxon, AmScope)  that make some moderate quality microscopes for not too-high-a price (~$1,500) that make good basic microscopy starter packs. Second-hand microscopes are fairly common on re-selling sites such as eBay too, just make sure you get to see/use it before purchasing.
Without knowing your use-case I can't make any recommendations on what sort of microscope might be useful for you if you were to get a replacement, but your "classic lab microscope" is known as an Upright or Compound microscope, used for looking at small things up-close with transmitted light giving you a flat 2D image. You might be familiar with stereo-microscopes, which are commonly used for looking at large objects up-close in 3D, usually using reflected light. Stereo-microscopes are also often used for things like soldering electronics and manufacturing quality control in textiles.

Thanks, I read your answer and I think I missed important details about the stand in my question. I have now edited the question and added these details.

In that case, given those details, in the absence of vibration, the image is probably as sharp as it gets. As I mentioned in my answer, this is not a professional microscope - those cost much much more than you payed - a medium-high quality single-magnification objective lens costs about the price you payed for the whole set-up!


text:
What is the mass of an E.coli cell?
I'm trying to get into Biology, reading introductory texts. A discussion on E.Coli estimates the mass of the cell from $$density =1g/mL=1g/cm^3$$ and $$volume=1µm^3$$ From this I get $$ mass=density × volume = \frac {10^{-6} g}{10^{-2}}=10^{-4} g$$ which is wrong since the answer is supposed to be $1pg$. What am I doing wrong? Thanks!

Its simple:
Mass = Density * Volume

= 10^3 (Kg/m3) * (10^-18 m3)

= 10^-15 Kg

which is equal to 10^-12 gram or 1pico gram

Wiki gives me micrometers to be $10^{-6}m$. And also that an $mL=cm^3$. Since I don't come from a background where units were ever used, can u please elaborate on how u got ur density and volume compared to mine? Thanks

@Craig Yes micrometers are indeed 10^-6 meters. But 1 micrometer^3 = (10^-6)^3 = 10^-18

10^-18 is in m3

Ahh... I should've paid attention in high school  physics


text:
What is the transcriptome in layman's term?
I am new to the bioinformatics field and am trying to understand a research paper that includes some terminology without definitions. The term transcriptome in particular is banded around in the literature, but is not clearly defined.
Can someone provide a reference or source to guide me to some learning material where I can get the basics.

Hi, welcome to Biology SE. Can you please clarify and refine your question? I`m not quite sure what you're asking, although I believe you would like to know what Transcription in RNA is.

Doesn't googling "transcriptome", help?

I've given a layman answer. With that information in mind you'll see that this is a big field and without the specific paper you had in mind, answering this question in the most helpful way isn't possible.

I would strongly recommend getting an introductory textbook such as Bruce Alberts' Molecular Biology of the Cell to help you understand all the various terms you are going to come across.

There are three "omic" definitions that might help you.
The DNA is the long term storage of the information. You're probably familiar with this concept, and the study of this type of information is genomics.
One of the major functions of DNA is it's use as the blueprint for the production of proteins. Proteins carry out all sorts of structural and functional roles in the cell. Which proteins are present at a certain times and locations is known as the proteome. This is studied in proteomics.
Inbetween the DNA and the protein is an intermediate step. The DNA is transcribed to RNA, and then the RNA is translated to the protein. During the transcription of DNA to RNA, certain sequences of the DNA are not transcribed to RNA for a variety of reasons. The study of what exactly is transcribed at what time in which locations is transcriptomics.

Also to include RNAs that do not give rise to proteins, DNA also serves as a blueprint for their synthesis.


text:
What types of species can produce genetically identical offspring?
Talking about identical twins, triplets, etc.  I'm curious which types of species are able produce genetically identical offspring.  Let's limit the scope to species that reproduce sexually and instances where the offspring differ genetically from the parents but are identical to that of at least one of their siblings. Are there phyla, classes, et cetera that do not ever produce identical twins?  Kingdoms?  Are there cases of plants producing genetically identical offspring?

you ought to clarify as well whether or not you mean fraternal versus identical twins (or higher level pregnancies) - - - many animals (e.g. cats, dogs, rodents) have "litters" of offspring, but whether or not any of those might represent 'twins' is probably difficult to tell (or not easily detectable)

Are you looking for a list of all known species that have been documented to produce twins etc? If so that is too broad a question. If not, it remains unclear what you're asking.

@James It sounds like they're asking which taxonomic groups are capable of genetically-identical multiple births, rather than a list of species. Which sounds to me like it could be an interesting question, except that I strongly suspect there will be some species in almost any higher level group for which they haven't been documented, so I'm not sure it's answerable in its current form. Maybe it could be edited to "what biological processes facilitate or prevent viable genetically-identical multiple births" or something - OP, would you be happy with that?

@arboviral That would be a more satisfying question.


text:
Why do earthworms have 4 hearts?
I was reading about earthworms and came to know that they have 4 hearts.
Why is there a need for a 4 heart system? What advantages would it have over a 1 heart circulatory system except for pumping more blood obviously.

The earthworm heart is not really like a vertebrate heart. They are not that efficient. More like valves you can say.

"pumping more blood obviously" Is it obvious? To me it is more obvious that there are way more factors in blood flow than the number of hearts. An interesting factoid though, I didn't know about this! You learn something new everyday they say, thanks.

Today suddenly many people are concern about heart :P


text:
How to do multiple sequence alignment?
I have a DNA sequence that makes protein 1. but now I have asked to:

compare the amino acid sequence of protein 1 with nine homologous proteins and make a multi sequence alignment (MSA) of the sequences.
Determine a consensus sequence for the proteins based on the MSA.
Find any specific parts of the proteins that are conserved, then explain why these parts are conserved.

Hint : http://www.bioinformatics.org/wiki/Multiple_sequence_alignment

A good start would be to load your sequence into an alignment tool/software. I would suggest using MUSCLE (http://www.drive5.com/muscle/). It is relatively easy to use.

MSA Tools

compare the amino acid sequence of protein 1 with nine homologous proteins and make a multi-alignment of the sequences.

EBI have a portal for many MSA tools and there are also other MSA tools available elsewhere.
In research, it's good practice to use several alignment techniques and look at which generates sensible indels. Usually, this is the lowest number of indel events.
Clustal Omega is probably the most sophisticated MSA tool hosted on the EBI site, however, it is relatively new and isn't as established as T-coffee or MUSCLE.
Note that these tools are updated fairly regularly. This question and top answer about "cutting edge" MSA tools from 2014 refer to a paper from 2011 that attempts to benchmark MSA tools. As you can imagine the state-of-the-art tools change rapidly (for example, clustal-w2 was released, and now clustal omega since that benchmarking paper). For most researchers though, it's a personal preference, and different MSA tools are "better" for different situations (speed of computation, number of alignments, similarity of sequences, complexity of secondary structure, local vs global alignments etc.).
Consensus sequence

Determine a consensus sequence for the proteins based on the
multialignment.

This depends entirely on the information from your alignment.
A common way to make a consensus sequence is to just take the most abundant residue at each position in the MSA. I don't like this approach because it heightens the significance of abundant residues, and diminishes the appearance of less abundant residues. This distorts the biochemistry and can easily lead to sequences that would be impossible or useless in biology. I would always rather see a raw alignment.
Conservation amongst alignments

Find any specific parts of the proteins that are conserved, then explain why these parts are conserved.

Conservation usually implies function, and hopefully you'll have a homologue that has a categorised function. Perhaps in your case one could attribute this function to a conserved sequence in the other homologues.
One brilliant tool is called consurf.

You can upload your MSA file to it and it will colour code regions of conservation from purple to blue. A purple region implies an evolutionary selection to not change that region, implying that it is a "functional" region.
Consurf works better with more sequences, so perhaps it isn't appropriate for this project. Instead try loading the alignment in Jalview and show "sequence conservation".

Caution.
When performing an MSA remember that the algorithm assumes that the sequence is homologous and that assumption can produce errors. If it looks wrong, it probably is!


text:
Are the ribosomes specific for each organism
If we removed one ribosome from human and we put it inside horse, would the ribosome perform the as it would in humans or it will not work or somewhere inbetween?

Welcome to Bio. It's best to ask one specific targeted question per post. I.e.  You might want to split them up. Second, a ribosome is huge. There's many things that gives it functionality. There is not something as the thing.

This sums it up https://www.quora.com/Do-all-ribosomes-in-the-plant-animal-kingdom-read-and-respond-to-DNA-in-the-same-way

First part is too broad and would essentially be considered a homework in this site. You should start with basic biochemistry and molecular biology (looking at your question I would also recommend you to read some fundamental organic chemistry. There are thousands of chemicals made of same atoms and sometimes even the same number of atoms [isomers] but still they are chemically very different).

One can prepare rabbit ribosomes from reticulocytes (immature red blood cells), and by providing a few cofactors required for an active extract, create an in vitro system that will translate virtually any eukaryotic mRNA that contains the correct sequence determinants. You can purify mRNA from your cells or tissues of choice, or you can synthesize an mRNA in vitro using a DNA template and an RNA polymerase. Either of these will be translated in a nuclease-treated rabbit reticulocyte lysate.
IVT (in vitro translation) extracts can be prepared from virtually any source (e.g., C. elegans shown by Bob Edgar in Cell ~ 1984). So I would predict that horse ribosomes would be happy translating human mRNAs, and human ribosomes would be happy translating horse mRNAs. The experiment you described, placing a human ribosome into a horse cell would be difficult to interpret because the endogenous horse ribosomes would already be translating the endogenous horse mRNAs, and so detecting activity from one additional ribosome could be challenging (even if you could come up with an experimental approach that gets that foreign ribosome in to the cell).
The take home message is that ribosomes, in general, do not care where the mRNA comes from--because ribosomes, as far as we know, do not have a way of distinguishing "self" from "other".

thank you for the valued information, actually my concern is if I want to think about the nature of the Ribosome, it would be chemical interactions at the end of the day right?,now, what is the thing that gives the result of the chemical interactions a behavior and function?

In an abstract sense one can consider the ribosome as an enzyme, an enzyme whose name would be something like polypeptide polymerase (or perhaps polypeptide synthetase). Now it happens that this enzyme has two rather large sub-units, and each sub-unit consists of a large structural RNA, plus dozens of proteins, but to answer your question, the ribosome has a catalytic reaction site, and it consumes substrates, and spits out products, just like every other enzyme. There is nothing magical. So your question becomes: how do enzymes work? You have the answer: chemical interactions.

what is the thing that gives the ribosome its functionality ( to synthesis the protein ).

RNA strands can fold themselves in a sequence specific manner. In fact ribosomes are highly structural being able to hold tRNAs having a hole which a polypeptide goes through during protein sysnthesis.

I do not know, but it could work. I do not know if it works exactly as horse ribosome works, either.


text:
How do house plants affect the quality of air in a house?
Do house plants affect the air in the house by taking it from the rooms and it is put in the dirt to make it moist then we have no air.

It is unclear what you are asking.

Plants have pores called stomata, where they generally intake CO2 from the air. There's a transport system in the plant called the phloem which pulls organic compounds down into the roots. When you have pollutants in the air that get sucked into the plant through the stomata, they get sent down to the roots. There are hopefully microbes down in the soil, and the harmful compounds get expelled into the soil, and broken down by the microbes. All the while, the plant is expelling oxygen. This should, in theory, improve the air quality.

I've often wondered, is this enough of a change to say that they "affect" the air quality. As in, "how many plants does it take to get a measurable difference?"

That's something to look into, I don't know the answer myself. In fact, the answer to OP was just an elementary plant structure-function overview.

In my oppinion you corrected and answered the question neatly. I was simply musing. Perhaps it's worth a new question.


text:
Can we predict a person's tolerance to cold exposure during excercise?
Being an amateur athlete and student of anatomy I've always wanted to know if there is a formula for determining an unconditioned body's tolerance to cold temperatures while exercising.
I know the factors of age,weight, gender, humid versus dry weather etc. are going to make it tough to determine.
Has there been any research into formulaicly describing a persons cold temperature tolerance?

Hi and welcome to Bio.SE! The original question invited homebrew formulas which could be opinion based. I've made an edit that asks for a more established method. Feel free to role back on the edit!

The first thing I'd look for is some kind of acclimatization index.  Even if all the other factors mentioned are the same, people living at different heights or different biomes (desert v tundra) will have different cold temp tolerance.


text:
Grouping OMIM disease codes
I have ~100 sets of genes, and each set includes between 2 and 70 genes. I'd like to perform an enrichment analysis on each of these sets to test if they're enriched for OMIM disease labels. However, I'm encountering a problem where the OMIM codes are too "sparse", such that each OMIM code only occurs maximum once in all gene sets. As far as I can tell, this makes the codes unsuitable for enrichment analysis in this case.
I believe that grouping the OMIM codes could solve this, as long as each group-label occurs multiple times in my lists. Grouping OMIM codes seems doable: for example, OMIM codes 601495, 613500, 613502, and 613506 all refer to types of agammaglobulinemia. I could imagine grouping codes based on something like gene ontology labels.
My question: is there a standard way to group OMIM codes?
I see some papers doing something like this, e.g. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4458913/, but I'm new to the field and don't know how "standard" approaches like these are.

Hi and welcome to Biology.SE. Without a clear scientific question to answer there isn't enough information here to answer the question.

Thanks for letting me know. I edited my question to include more information. Let me know if I can add more.

It's still hard to tell exactly how you want to group them and to what end, so I've provided a general answer below. I hope it helps!

Based on OMIM ID codes
In a broad sense NIH have already divided the IDs. If all you are checking is OMIM code enrichment, this might be an okay resolution since it can tell you the chromosomal locus (autosomal, sex linked, or mitochondrial).

Each OMIM entry is given a unique six-digit number as summarized below:
1----- (100000- ) 2----- (200000- ) Autosomal loci or phenotypes
(entries created before May 15, 1994)
3----- (300000- ) X-linked loci or phenotypes
4----- (400000- ) Y-linked loci or phenotypes
5----- (500000- ) Mitochondrial loci or phenotypes
6----- (600000- ) Autosomal loci or phenotypes (entries created after
May 15, 1994)

Other databases as an alternative method.
If you are interested in specific phenotypes, you may need to get more involved.
OMIM doesn't really attempt to group diseases together beyond their ID nomenclature as far as I'm aware. There have been several projects that set out to do this, like the one the question points out, and the examples below. They mostly use phenotypic data in combination with OMIM information.
Two databases that aim to solve this are:

HPO
LDDB
Enricher web-server see @MaximKuleshovs answer below!

These are tools with controlled vocabulary for phenotypes and associations from OMIM codes. They could help you check for disease/phenotype specific enrichment. This would certainly allow programmatic grouping, although I have not worked with either before and I presume it would be very involved!
It's up to you!
Wikipedia has a list of OMIM codes listed in alphabetical order if you wanted to try to group them manually by whichever criteria you desire.

Without your source code it's hard to tell, but maybe the maximum of one occurrence rate could be a code problem rather than a scientific problem.

Thanks very much! That's exactly what I was looking for. I tried grouping by different arrangements of the numerical OMIM code (include using the first digit) but I don't think it makes much sense for my application. I'll look at other databases and/or try a custom solution.

There's an approach from "Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool" paper:

The OMIM gene-set library was created directly from the NCBI’s OMIM
  Morbid Map. We removed diseases with only a few genes and merged
  diseases with similar names because these are likely made of few
  subtypes of the same disease. In addition, since most diseases have
  only few genes, we used our tool, Genes2Networks, to create the
  OMIM expanded gene-set library. We entered the disease genes as the
  seed list and expanded the list by identifying proteins that directly
  interact with at least two of the disease gene products; in other
  words, we searched for paths that connect two disease gene products
  with one intermediate protein, resulting in a sub- network that
  connects the disease genes with additional proteins/genes. Each
  sub-network for each disease was converted to a gene set.

Enrichr itself has two OMIM libraries in Drugs/Disease categories. Moreover it has Human Phenotype Ontology library and MGI Mammalian Phenotype libraries.


text:
How to batch convert gene names to protein IDs in Uniprot?
I have a list of >1000 "ordered locus names" from the STRING database (also called gene numbers, ORF numbers, or CDS numbers by uniprot). They're in the form of 'b0014', 'b0015', etc. I'd like to convert them all to Uniprot protein IDs.
I know how to do it in a non-batch way, since searching Uniprot for 'b0014' returns what (I think) is a protein ID. However I'd like a batch solution since there are so many IDs that need converting.

http://www.uniprot.org/help/programmatic_access

also cross posted here

@MattDMo Thanks. I haven't tried it yet, but the solution that looks like it will work is the UniProt ID converter http://www.uniprot.org/uploadlists/.

ID mapping
This is called ID mapping. It used to be a headache as programmatic sequence comparisons were the only real way, but it is pretty trivial these days.
As mentioned in the comments, by far the most popular and easy method is to use Uniprot's list uploader for mapping. The corresponding publication can be found here.
Example
Programmatic access
The web user interface will work for thousands of IDs, but is like to result in errors for queries exceeding 10,000 IDs. In that case programmatic queries are probably better. I've slightly modified this from the Uniprot docs so that the IDs are queried 1 at a time to avoid any errors in exceeding query size. The python code would be:
import urllib,urllib2

list_to_convert = ["b0014", "b0015"]
url = 'http://www.uniprot.org/mapping/'

print "From To"
for genename_id in list_to_convert:
    params = {
    'from':'GENENAME',
    'to':'ACC',
    'format':'tab',
    'query':genename_id
    }

    data = urllib.urlencode(params)
    request = urllib2.Request(url, data)
    contact = "" # Please set your email address here.
    request.add_header('User-Agent', 'Python %s' % contact)
    response = urllib2.urlopen(request)
    page = response.read(200000)
    print page.splitlines()[1] #Ignores the header line returned by uniprot

The output from this looks like:
From    To
b0014   P0A6Y8
b0015   P08622

Web GUI
b0014 and b0015 aren't actually STRING IDs. They are IDs referred to as gene names and are used across a variety of databases including Uniprot.
The mapper:

Note in section 2 of the ID mapping that I have set the left option to "gene name". "STRING" won't work.
The result is below:

The first answer is good!
Here I want to suggest another useful tool when you are thinking about ID Mapping.
That is bioDBnet: db2db, which is used for "Database to Database Conversions".
The introduction of this tool is:

db2db allows for conversions of identifiers from one database to other
  database identifiers or annotations. To use db2db select the input
  type of your data, changing the input type automatically changes the
  output options to the ones specific for the input selected. Then
  select one or more output types and add your identifiers in the ID
  list box. Set the remove duplicate values to 'No' if you do not want
  duplicates to be removed. Clicking on submit then returns a table of
  your inputs matched against all the outputs selected in the exact
  order as entered. Results can be limited to a particular taxon by
  entering it's Taxon ID. The performance will vary widely depending on
  the number of outputs and the options selected. Conversions to a
  single output with the default options should complete in a few
  seconds

The above is my favorite tool, and sometimes using from ensemble will help you solve the problem in a more efficient way if you are dealing with model organism, like mouse and human.