evolution - From which ancestor species did humans inherit orgasm?

Let's assume that pleasure from sexual intercourse might be indicative of some sort of orgasm. Then this would suggest that any evidence of autoerotic behaviour would point to the existence of orgasm, or certanly physical pleasure.

I found this quotation on the Wikipedia page for Animal sexual behavior, amongst a lot of information about mammals :

Many birds masturbate by mounting and copulating with tufts of grass, leaves or mounds of earth...

apparently from Bruce Bagemihl: Biological Exuberance: Animal Homosexuality and Natural Diversity. St. Martin's Press, 1999. ISBN 0-312-19239-8

If this is taken to imply that the last common ancestor of birds and mammals experienced this pleasure then we have got fairly deep into evolutionary history, although not as far as fish.

genetics - Mapping a mutation to known SNP, 3' UTR, miR

I've parsed out a very large TCGA cancer ssm (single mutation file) file to give me the essential information.

The ssm is in the following format:

['Gene name', 'Ensembl Gene ID', 'Chromosome', 'Chromosome start', 'Cancer Type']
['NTRK1', 'ENSG00000198400', '1','156849827', 'Prostate Adenocarcinoma (TCGA, US)']

From there I would like to grab each mutation and :

1. Map the chromosomal position to a known SNP (rs something output).


2. See if this snp is found in a 3'UTR


3. See if this snp is found in a miRNA


4. Missense or sense mutation


5. Any relevant genbank etc.. ids

I'd like to do this Python (I think BioPython is suited for this) for downstream applications.

biochemistry - During starvation, does the human body do anything to prioritize which organs receive nutrients?

The glycogen in the liver begins providing blood glucose. Muscle glycogen is used as fuel by the muscles, fat cells (adipose tissue) release fatty acids to manufacture ketone bodies in the liver and to be used by the brain as fuel, and body proteins are converted to glucose.

In short, the body's metabolism shifts to catabolic reactions.

If this continues for too long, you begin to see effects of starvation:

• Inadequate tear production


• Enlarged/tender liver


• Muscle atrophy


• Rashes, sores, or peeling skin

In short, deficiencies of energy, protein, iron, and zinc can really mess you up in the long term.

cell biology - Improving transformation efficiencies- induce supercoiling?

From my limited knowledge of science, I know transformation can be one of the hardest step in cloning, and that a large amount of research/trial and error has been done to improve on this step. I've heard electroporation is the most efficient technique, though I have no reference, and of course the cell, media and duration all have vital parts to play in the process.

However, I've never heard of supercoiling as an important factor. Size of the plasmid plays a large part in transformation, so intuitively it makes me think supercoiling the plasmid prior to transformation would improve the efficiency. I thought transformation was simply DNA diffusing through holes, but are parts of the plasmid required to bind/interact with the host?

Why aren't we suggested we supercoil prior to transformation? I have several thoughts but I'm just guessing:

• Is it because gyrase can disrupt the integrity of DNA?


• Or is it that it's just an expensive enzyme and the gain isn't worth it?


• Or perhaps supercoiling reduces efficiency of subsequent plasmid preps/transcription (though wouldn't the host's natural enzymes supercoil anyway?)

lab techniques - How long can I store autoclaved disposables and reagents?

Not really an answer I know, but too long for the comments...

This is still too broad a question. a well sealed, sterile plastic usually has a use by date, but can probably be used more than a year after you receive it. But these cases are not usually the issue.

Its sterile medium and chemicals, each of which needs to have their own due date. LB can be used months after autoclaving, but antibiotics break down chemically in weeks (ampicillin 1000x stocks lose their potency in a month). Even in the refrigerator Agar plates show colonies after a couple of months and dry out quickly.

So more details would be necessary and the case by case policy is the rule.

added in response to comments

Its really a matter of how well they are sealed. An autoclaved bottle will stay sterile forever, until something gets into the bottle - it depends on how well you have sealed things up and the storage conditions. For stuff sterilized in lab I would tend to use it within a couple of months. For eppendorfs we'd tend to sterilize a few hundred in a beaker and not worry about them...

Our experiments were working with purified protein were only medium sensitive to bio-contamination; they would be done in a few hours and then sterile filtered again. If you were purifying RNA for instance you would be much more paranoid I'm sure.

If you start to see contamination I would lower the use date and or improve your protocol.

Plastics that come sterilized and sealed by the manufacturer in 3-5 mil plastic bags have really long use by dates and I've used them for up to a year after we received them.

brain - How do we memorize something?

The current working theory (note this is still an open question, but there are many leads being followed):

Sensory systems receive a combination of signals from an event, which are initially bound to the hippocampus (this is called episodic memory). Then, typically during sleep, the memories are consolidated.

A simplified view is that consolidation basically consists of communication between the neocortex and the hippocampus, and the memories are thought to be "saved" in the neocortex. Thus, amnesia patients with hippocampal damage still have all their long-term memories, they just can't create new memories (because their old memories were already consolidated to neocortex).

Your neocortex has many subregions with many functions. One is the temporal lobe, where semantic memory seems to be stored. So your episodic memory may record several interactions apples and, over time, your semantic memory will be updated (as memory consolidation occurs) to "consolidate" your concept of "apple".

The temporal lobe is highly connected with the occipital lobe (where visual information is processed) and the two likely work together to identify objects using the consolidated information.

On the molecular level, how the memories are actually stored. The most well known concept is connectionism: different connection strengths between neurons carry different information. But there's also genetic expression going on, and there was recently some research on prion-like proteins contributing to memory as well as astrocytes.

Realize, of course, that a lot of this is cutting edge research... and therefore could be wrong or contain numerous oversights and simplifications.

perception - How can you test what color different people perceive?

It's impossible to be sure how another individuals brain represents the world. For all we know, they way they sense depth and up and down might be completely different. The representation of colour could be completely different. Both individuals could explain it as images, but if it were possible to move another individuals representation into another individuals brain - it's likely the other individual would experience an abstract sensation that would be difficult to compare to anything else that individual has experienced.

It could well be like having a compass attached to your body, sending nerve signals to your brain. You would not understand how to interpret it unless your brain has plenty of time to associate the stream of signals of direction with other signals such as your balance, vision and audio.

The brain is a very complex organ, and it probably starts out like a tiny, one celled blank sheet of paper. That blank sheet of paper is receiving continous streams of electronic signals from the various sensory organs of the body. Over time, synapses between your neurons will bond with other synapses, due to both of them receiving signals simultaneously. For example, if you are listening to music, you will hear various frequencies. Usually there will be a drum beat, which you will also sense as vibrations in the floor and your stomach. The neurons handling those two different signals will then bond together, so that at a later time - when you sense bass signals in the floor, but not in your stomach and by your ears - your brain will still recognize that drum beat in the floor as music. Some people might even feel like they hear the music.

The nerves are then going from the sensor to the brain in various ways and paths, and those connections are different for everybody.

Your brain will visualize stuff your way, and other people will visualize stuff their way and I believe those representations of objects and things are completely different for everybody. The representations will be compatible among different people, in such a way that physical laws are obeyed - but that is because the brain alters representations according to previous experiences.

So, knowing that it is impossible to be sure, I really do believe that everybody represents sensations completely different. They will be handled in similar regions of the brain due to physical similarities of the body, but within those regions in the brain there will be huge differences in representations.

I believe that if a human, unknowingly had a compass operated into his body at birth and connected to an arbitrary nerve, then that human would experience a heightened sense of direction that it could not explain as an adult. If another human had an identical compass attached to a completely different part of his body and connected to perhaps the nerve going from one of the ears, then that human would experience the same sense of direction.

Disclaimer; I am a computer programmer with a keen interest in virtualized intelligence - I have no education in the area of biology. :-)

botany - How to distinguish those flowers in outskirts: hawkweeds (Hieracium), hawksbeard (Crepis) and hawkbits (Leontodon)?

It's quite hard to answer this question and the best would be to follow a flora, which I'll not just copy informations from to past here.
So following are general observations subject to numerous exceptions.

Hieracium generally have lanceolate to oval leaves, not or little toothed, most hairy.

Crepis and Leontodon have generally Taraxacum-like leaves, that means, dentate to lobed.

Some Crepis have leafy stems (but some don't), while Leontodon always have their leaves concentrated to the base, forming a rosette.

[edit on 2014, october 2]

Be aware that there is another genus of the Asteraceae family which may be mistaken with the Crepis/Leontodon/Hieracium group, although it's easier to distinguish. It's the Hypochaeris genus.

Hypochaeris have few but not so homogenous species as there are within the other genera.
Hypochaeris radicata (which may be the most common species in France and wester Europe) have all its leaves basal, forming a rosette and sticking to the ground (never erected). These leaves are always lobed (neither entire, nor toothed), with erected hard hairs covering there upper faces.
Hypochaeris maculata may be mistaken with some Hieracium : it have hairy smooth entire leaves wich are (all or mostly?) basal forming a rosette.

[Addition on August, the 5, 2014]

Also Leontodon and Hypochaeris have hollow stem just below the capitulum(1). When you press the stem just below the capitulum, you fell it flattens under your finger, and if you use the nail to make an incision in the stem, you will see it is hollow like a pipe.

NB : Taraxacum also have hollow stems but they are fully hollow (from the base up to the capitulum), while Leontodon just have the upper part of the stem which is hollow.

Leontodon are almost always monocephal, that means, the stems are not branched : they have only one capitulum per stem, while Crepis and Hieracium and Hypochaeris mostly (if not always) have branched stems carrying several capitula.

(1) the capitulum is the type of inflorescence in the Asteraceae family. It's also called "head" (and actually, "capitulum" is the latin word for head).

You may like to have a look at this page [in french] presenting some common yellow and ligulate weeds from the Asteraceae family to get some illustrations of what I explained here.

molecular biology - Problem on finding sequence of Taq polymerase

According to the paper here "Taq polymerase" is the DNA polymerase I from Thermus aquaticus. (Incidentally the paper has the complete sequence of the gene in question.)

You can find a protein sequence entry at NCBI here. This shows the sequence of amino acids in the protein, not the DNA sequence of the gene. Several lines from the top you will see:

DBSOURCE locus TTHDNAP accession D32013.1

with the last word highlighted as a link. Follow that link to the DNA sequence. That entry includes the line:

CDS 1..2499

which tells you that the initiator ATG of the gene is right at the start of the sequence shown, but that the 3026 bp sequence includes a lot of downstream DNA. If you click on CDS on that line it will highlight the coding sequence in the DNA.

A very cursory comparison of this sequence with the one in the paper that I linked to suggests that this is the same gene.

human biology - In theory, would it be possible to create an injection of Vitamins, Minerals, sugars etc so that eating was no longer necessary?

I am wondering, out of pure curiosity, whether with current medical & biological science, (or indeed with accepted probable future developments in those areas), in theory, would it be possible to create an injection of vitamins, minerals, sugars etc so that eating was no longer necessary, and in fact, an average life with average energy usage could be continued?

I am not a biological professional nor academic, however I thought this was closest to the mark. If there is somewhere more appropriate please direct me, and I shall delete the question and post it there.

Also, if no, would there be certain parts that you couldn't replicate in an injection or something of the like?

NB: This doesn't have to be an injection, any simple method of ingesting or attaining everything the body needs. This could be a pill, or anything. I simply used an injection as an example.

Thank-you very much.

Edit:
Having found this question,
Has there ever been an attempt to create nutritionally tailored food for adult human consumption?
I would like clarify. This has given me a lot of information, however, I am looking for any method APART from food. Thanks.

gene expression - How can a continuous RNA be transcribed in the lac operon?

RNA Pol doesn't worry about stop codons. Transcription termination can occur through the formation of a hairpin in the new RNA sequence, or through the action of Rho proteins. A lot of the time prokaryotes have polycistronic mRNAs, that is, mRNAs with multiple protein coding regions. The stop codons are detected during translation, so you will often have all three lac proteins being translated at once off of the same mRNA.

Here's a nice section on transcription termination, or look up Rho-independent or Rho-dependent transcription termination for more info.

ecology - What type of biome is this?

Well, first of all 812mm is a pretty precise value to be preceded by the word "about". "Mildly hot", on the other hand, is too vague a term for your question to be answerable. If you update your question with better parameters, you may get more helpful answers.

In any case, according to this page, a tropical savanna has mean monthly temperatures at or above 64°F (~18°C), which may or may not qualify as "mildly hot" by your standards, and annual precipitation averages between 30 and 50 inches which means between 762mm and 1270mm.

So, I what you are describing could be a tropical savanna, but as I said before, I can't tell unless you update your question with more information. Have a look at this site, it may be of help.

species identification - Strange looking mushroom found in a dead tree

I'm trying to identify this mushroom my sister found at her campus' lawn. It is brown, looks somewhat like a turtle or a brain and is growing inside of a dead tree trunk. Geographically the campus is in Haifa, Israel in case that helps. Any ideas?

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