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Jan
28
comment Is ginger a vegetable?
Technically what you eat of ginger is not the root, but the rhizome (en.wikipedia.org/wiki/Rhizome), which sets it apart from carrots. The ginger plant is defined as a flowering plant, how cooks define ginger I can't tell. I would guess as a spice.
Jan
28
comment Is urine sterile? A reference request for evidence supporting sterility
As there definitely are uropathogens, you can at least be sure urine is not always sterile. I have heard people talking about obligate pathogens in the urine and they definitely found microflora in healthy urine. But that was personal communication (and as far as I know the group studying their own urine because they needed to know whats there before using it to grow other bacteria, so not a study setting to be published).
Jan
19
comment Why does the open tree of life have 2600 species of rose?
OTT does not claim the taxonomy to be perfect, as it was generated by a synthesis of a lot of existing taxonomies. This might lead to an overrepresentation of some species/subspecies, because they have been classified differently in different taxonomies.
Dec
8
comment Why do PCR manufacturers recommend assembling the reaction mix on ice?
As I was told as an undergrad, polymerase is thermostable but it could also activate on room temperature. As you are carefully going to cycle between temperatures, you don't want the reaction to start early on room temperature.
Nov
26
comment Question regarding research project on indigenous ants during Eastern European winter
If that is enough for you, you can actually buy complete ant farms.
Nov
23
comment How much genomic variation one usually find within a given bacterial species?
Be careful! As bacterial genomes are circular and we have to write down their nucleotide sequence as linear, the "break point" of the circle does not necessarily have to be in the exact same point for two genomes in the database (as it is kind of based on the assembly where a break would be, unless you manage to end up with a fully circular genome and can decide). Therefor, while the sequence in question might not have changed, the nucleotide in question could still be in a different "position". And otherwise: that depends. Some genomes are more stable than others. Some genes are, too.
Nov
20
awarded  Necromancer
Nov
16
comment Homeopathy is placebo, but isn't placebo good?
I would consider making somebody else believe in something that does not work morally wrong. If there is another treatment option that works, it might keep them from using it (or if they try both at the same time, might interfere in the worst case). If there is no other option, you give them a false hope of healing. For yourself, feel free to try. I have trained my mind on homeopathic tablets to believe they make me more focused. I know it is just sugar, my subconscious is tricked into focusing. It might be a Pavlov's response to the taste of those tablets. As it works, I don't care.
Nov
12
answered Does the location of the double bond in chlorins yield a distinct biological function?
Nov
11
comment Is the prostate problem unique to humans?
I love your two answers to the why question!
Nov
11
comment What is this stick-like creature?
I must say, I am impressed. This might be the most stick-like stick-like insect I have ever seen. Complete with ends that look like they broke off a longer stick. (I do not doubt it is an insect, if it moves when poked like you describe. I am really impressed.)
Nov
11
comment Why do we generally sleep with our head facing away from the door?
One question... do you mean facing as in "looking in the direction" (then it seems you already found two people, three if you include me which actually do face the door. Or do you maybe mean "facing the door" as in "you head being closer to the door than your feet, so the back of your head is in the direction of the door"?
Nov
11
comment How thick is the residue from a fingerprint?
Wouldn't that depend a lot on your skin type, how moist your skin is, what stuff you have touched before,... ?
Nov
9
comment GC-Content bias and length bias in TCGA RNA-seq level 3.0
I am not sure about the "level 3" but looking at their website "level 3" in RNAseq data can mean very different things. Generally it is the already calculated expression signal, but some of the datasets are normalised, others are not (at least it is not explicitly stated). So I guess you cannot generally conclude which steps of preprocessing have already been applied to the data.
Nov
9
comment If all bacteria in human gut are dead, can they be there again?
The article ( as far as I understood from quickly scanning over it) is more about bacteria in your gut generating cravings for different types of food. The ones "liking chocolate" are more likely to like high-sugar food. If you wouldn't eat any sugar at all, some of them might die out, but others will be able to utilise other nutrients. (Very, very basically said.)
Nov
9
comment Difference between sequence alignment and sequence assembly
Both comparisons are nice, but only half of the truth. I can do alignment of two puzzle pieces (pairwise alignment) without a reference. And I can do reference guided assembly (what you describe is de novo assembly), by using alignment to a closely related reference as a guide for assembly. ( so assembly with a picture that does not show the current puzzle, but a similar one).
Nov
9
comment Difference between sequence alignment and sequence assembly
@Dexter Again, it is not. Sequence alignment is a part of sequence assembly algorithms, but that does not make assembly a special case of alignment.
Nov
5
comment Is there a lower temperature limit, below which we cannot sense a difference in temperature?
I always hated opening the -80 freezer, because it felt... just incredibly cold! (With protection, but obviously not to my face over the freezer.) You just touched something shortly, probably with a short area of skin contact. With larger area of contact and longer exposure you will feel the difference. Like it is the case for hot things. But as far as reflexes go, you're supposedly already letting go/getting away before you really feel the full cold/heat.
Nov
4
comment Please explain this disrepancy about ageing
I think the problem is that you mix up the ageing of a cell with the ageing (or life span) of an organism. Of course the maximal lifespan in a perfect environment could be based on telomere length, but there are other factors shortening this life span as health care, general safety, behaviour,...
Oct
29
comment How do you create a .snp datafile?
You will have to detect SNPs. You can get the vcf by aligning your resequenced fastA to the reference genome (or previously sequenced genome) and use a Variant Calling method of your liking. Then there is this tool to convert vcf to the required .snp file: github.com/loire/vcf2DIYABC.py