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How do SDS-PAGE gels differ in a Bis-Tris system vs. a Tris-Glycine system?
Protein migrate differently in Bis-Tris and Tris-Glycine gels. I was curious about the actual reasons why. Do certain gel systems result in a tighter resolution than others?

SDS PAGE system rely on the fact that protein is denatured and surrounded by the SDS negatively charged detergent micelle.  This eliminates most of the charge and idiosyncratic solubility differences from one protein to another and gives a reasonable separation based only on size of the protein which is related to the size of the SDS micelle around each molecule.
Bis-Tris and Tris-glycine buffers have quite different charge shielding characteristics.  Bis (also known as 2-[Bis(2-hydroxyethyl)amino]-2-(hydroxymethyl)-1,3-propanediol) has a tertiary amine with a pKa of 6.46 and a pKb of 7.54.  glycine is a zwitterion at any pH between 2.3 and 9.6.  This creates a difference in the way that the buffer shields the SDS PAGE micelles from the rest of the electrical field, slowing down (probably glycine slows things down a bit) the time to resolution, but also giving the micelles more time to migrate.
So for SDS PAGE systems, the resolution of the gel has at least as much to do with the size of the gel pores (based on the acrylamide and bis-acrylamide percentages), the amount of protein you are putting into a given volume of loading well, and the size differences of the bands you are tying to separate. (you need to get pretty lucky to separate a 100.54 kda band from a 100.85 kDa band, but 1.5 to 1.8 kDa is easier 10 to 14 kDa is even easier). Also consider adjusting the current or voltage of the power supply.  The buffer system is only one consideration in planning your experiment and often not the primary factor of quality.


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What is the difference between HPLC and FPLC and why is FPLC preferable for protein purification?
I've used HPLC (high performance liquid chromatography) before (once, so I'm barely even qualified to know what it stands for) so I was surprised when my labmate told me she would be using an alternate technique to isolate a protein.
What exactly are differences in HPLC and FPLC (fast protein liquid chromatography) instruments, and why would FPLC be a better technique than HPLC to use with proteins? What situations make HPLC preferable?

The only difference between FPLC and HPLC is the amount of pressure the pumps apply to the column. FPLC columns have a maximum pressure of about of 3-4 MPa, whereas HPLC columns can withstand or require much higher pressures. As a general rule, HPLC columns won't work with old FPLC equipment; FPLC columns can go on HPLCs as long as the pressure can be regulated.
Manufacturers have been marketing separate equipment to handle these different classes of columns, but the trend seems to be heading towards machines that can handle both types of columns without issue. A GE rep told me a few years ago that they've improved the pumps on the AKTAs to the point that "they're technically HPLCs now." The term "FPLC" is probably on its way out.

I wouldn't say that's the only difference, but it's a large difference. Most of your HPLCs will expose the compounds to several metal components, which can denature some proteins, while FPLCs are designed to minimize metal exposure and preserve protein structure better. HPLCs usually have better detectors, often with monochromators for full wavelength selection, while basic FPLCs have simple detectors with 2 wavelengths, 254 and 280nm, which is usually fine for proteins. Reverse phase HPLC will often use organic solvents, while FPLC usually uses buffered aqueous solutions.

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How does Serotonergic (5-HT2A mediated) Psychedelia work?
How does serotonergic (5-HT2A specific) psychedelia work? I've read that there are some theories that it might involve the induction of a glutamate release in certain regions of the brain involved in perception.

Brenton, the linked pdf is called "Multiple receptors contribute to the behavioral effects of
indoleamine hallucinogens". It goes into detail on a a few basic behavioral responses.  I don't know what your background is so if you need help understanding parts point them out to me and I'll give it a go.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3110631/pdf/nihms267079.pdf
https://docs.google.com/file/d/0B0JUrCVOms3MdzdlYmh0SnBmOHc/edit (I'm hosting the pdf on my Google Drive if you aren't able to see the link hosted by the NIH).

Thanks, mate, if I find the article in question sufficiently helpful I'll accept your answer and up-vote it. I'm grateful that you quoted a reliable source. Of course you can't just take people's word on these Q&A sites without some proof because you can't be certain of their qualifications regardless of what they claim. I probably won't need too much help in understanding it, I usually understand such articles, but if I need help I'll ask.

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Why does cyanide inhibit CuZnSOD, but not MnSOD or FeSOD?
Different types of superoxide dismutase (SOD) contain different metal ions (Zn, Cu, Mn, Ni, or Fe), all of which allow them to catalyze one reaction, dismutation of superoxide anion, O2−. Cyanide can block this reaction, but only in CuZnSOD.
What is the (bio)chemical mechanism behind cyanide inhibition of CuZnSOD and why doesn't it occur in FeSOD or MnSOD?

It would be nice if you could add some references to your question.

I'm just taking a stab, because my inorganic chemistry is rusty.
cyanate (CN-) is well known to bind to iron (it inhibits hemoglobin and causes anoxia), and it also forms a pretty strong complex with Zinc:
http://en.wikipedia.org/wiki/Zinc_cyanide
I would guess that in the case of the SOD that the other liganding amino acids and the pocket of the enzyme are such that the affinity for cyanide is lowered to the point that oxygen can displace it.
In the case of hemoglobin, CN will coordinate to the heme iron in much the same fashion that O2 does, but it doesn't come off.   In the case of SOD, the enzyme will be looking to coordinate to superoxide O2(2-) which would be at a roughly tetrahedral angle to the metal.   This is not a favored geometry for CN coordination, which prefers to linearly coordinate to things.
In the case CuZnSOD it seems likely that this enzyme has enough room and its Zn and Cu binding envirionments don't forbid CN binding. it would be an evolutionary accident really as to why one is sensitive and another is not.
some structures at rcsb:
SODs:
http://www.rcsb.org/pdb/results/results.do?qrid=C0740111&tabtoshow=Current
thiocyanate bound. the pocket is pretty open between the two ions.  no CN bound structure.
http://www.rcsb.org/pdb/explore/jmol.do?structureId=1SXS&bionumber=1

One can argue that only the "eukaryotic" types of SOD are sensitive to cyanide treatment:

FeSOD is designated as "prokaryotic" type of SOD which is uncommon (but possible) for eukaryotes (reference).
CuZnSOD is a cytosolic SOD, whereas MnSOD is located within mitochondria (reference). Taking into account the endosymbiotic theory we might also suggest that MnSOD is also a sort of "prokaryotic" SOD.

This answer is not yet a biochemical mechanism.


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Function of an VEGF inhibitor in the treatment of macular degeneration
I'm working on a short presentation of treatments of macular degeneration for a biomedical
optics seminar on macular degeneration.
Since I don't have any relevant medical or biological background (B.Eng. Electrical Engineering, now M.Sc. Biomedical Engineering w. a major in Biophysics) I need some help with
understanding the function of VEGF inhibitors, and how they work.
It doesn't need to go into all details as it is one of three treatments that I'm supposed to present, but enough to explain how it works, in about roughly 5 minutes.
Could anyone help me please?

The Wikipedia page for vascular endothelial growth factor (VEGF) looks pretty useful - it explains that VEGF stimulates the growth of blood vessels. If this gets out of balance, for example in diabetic retinopathy and wet form age-related macular degeneration, one treatment is to attempt to reduce levels of VEGF in the circulation, using monoclonal antibodies directed against VEGF, or to antagonise the action of VEGF using drugs that target the VEGF receptors.
Two milestones in anti-VEGF therapy are described in these papers:

Ng et al. (2006) Pegaptanib, a targeted anti-VEGF aptamer for ocular vascular disease. Nature Reviews Drug Discovery 5: 123-132 (This paper describes the first approved aptamer drug: an RNA directed against VEGF.)
Ferrara et al. (2006) Development of ranibizumab, an anti-vascular endothelial growth factor antigen binding fragment, as therapy for neovascular age-related macular degeneration. Retina 26:859-870 (This paper describes a therapy based upon an antibody fragment directed at all isoforms of VEGF-A.)

A very recent review of anti-VEGF therapies is:

Freund et al. (2013) An update on the pharmacotherapy of neovascular age-related macular degeneration. Expert Opinion on Pharmacotherapy 14:1017-1028


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Why is it sometimes difficult to resuspend E. coli in P1?
It's a curiosity question. When I'm doing minipreps after pelleting the bacteria sometimes it's very easy to resuspend them in P1 (Qiagen kit), but sometimes they form a rubbery clump that is very hard to break up with a pipette and I have to vortex the tubes. It interests me because it adds more time to my lab work and I wish I could avoid it.

how old/dead are the bacteria?  resuspending fresh pellets seems easier to me..?

Straight from 16h culture.

When I do giga preps, I have to weigh the pellets and put 7g of cells into a 1L pyrex bottle, then add the P1 and a small stir bar  that helps beat the pellet apart with vigorous mixing. Using more than 7g can overload the column with DNA and give a poor yield.

This is particularly an issue when you do maxipreps and the pellet is 200x the size of the pellet from a miniprep. The reasons why? Maybe you're pelleting at too high of a g-force (pure speculation). Alternatively, you could be growing the cells too long. I typically miniprep after a 12 hr culture. If you're seeing any darker colors in your pellet, you have a significant amount of dead cells. Those dead lysed cells will spill out their genomic DNA which is very viscous.
For maxipreps, you can't break up the pellet merely by pipetting up and down a few times and calling it a day. What you can do is swirl the side where the pellet is and breakup the clumps. Alternatively you can use a different pipet tip (for an extensive discussion on this very topic see Pipetting damage to cells). I change to a P200 for my minipreps and pipetting only the area around the pellet seems to do the trick for me. For maxipreps I use a P1000 which is better than using a 5mL syringe.

I don't think that the pellets are darker, but I've noticed that sometimes the shaker causes my tubes to screw themselves. Could it be because they don't get enough air?

@MaciejTrybilo, what is your final OD?

I'd have to measure next time. What would you consider excessive?

It depends on your cells and what media you're using. The OD is more to check about the aeration. A lower OD would indicate that. Too high? Maybe use more P1.

@MaciejTrybiło  more areation is better. If your tubes get lose maybe they get more shaking, therefore more areation and so faster growth. And the ratio surface for volume matters here. That's why I always use 50mL Falcon tubes even for 5mL cultures.

@carandraug I also use those. I leave the caps loose and I notice that sometimes the shaker causes them to screw on quite tightly. Even though they seem to grow well (the culture is very cloudy and I get a decent size pellet) I was wondering whether it made them switch completely to anaerobic respiration and cause this gummy pellet somehow. Just a thought.

@MaciejTrybiło nah! That shouldn't be a problem. I always close the tubes very tightly, afraid as hell that the tubes will open and I get contamination.

Are you pelleting using a swinging bucket centrifuge and the 50 mL falcons? If so, then the pellet should be squarely in bottom. That should make things easier.

Some things to consider. If you spinning too fast and too long, that is going to pack the pellet more. You can spin longer at a slower speed and you will notice your pellet is not as tightly packed. I always do 2000 rpm, 20 minutes, 4C if I'm doing a midi or maxi sized prep and harvesting bacteria in a 50ml conical.
If I'm doing a miniprep I will take the 1.5 micro centrifuge tube (with pellet and buffer p1) and scrape the bottom of the tube 1 or 2 times across all the holes in the rack. This vibrates the tube good loosening and breaking up the pellet. You can consistently perform this step across many samples, this does a good job of re suspending the bugs.
I have noticed that cultures that are overgrown, contaminated, or grown in incorrectly formulated lysogeny broth, will give the pellet some weird characteristic including color and the pellet 'texture.'

What I do to avoid this is to ressuspend the cells by pipetting up and down the P1 (ressuspension) buffer on the side of the tube. This way, every time takes only a bit of cells every time and big clumps are avoided. The  only times I used to get big clumps hard to ressuspend were when I went poking at the pellets first.

Yes, I do that too. In the situations I'm talking about, rather than slowly breaking up into a cloud, the pellet will unstick as a whole from the bottom of the tube and clog the tip.


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Using ion-exchange chromatography to purify DNA from a cell extract - Is DNA more negatively charged then RNA?
When applying this method we have a glass or plastic column of resin which is positively charged. Then we pour cell extract into the column in order to capture the negatively charged particles which include DNA.
After that we gradually add salt which neutralizes the molecules. But it does this gradually so strongly attached DNA molecules fall last while RNA and proteins fall first.
The question is why does DNA have a greater negative charge than RNA ?

Perhaps this could be due to the size of the molecules? DNA is double stranded vs typically single stranded RNA and DNA is also more stable so would probably be longer.

A longer or duplexed Nucleic acid will have more charge per mole of the molecule. But generally it is not the overall charge that matters in electrophoresis or MS or chromatography; it is the charge density and specific charge (z/m) that matters (charge density of a longer RNA will be almost same as smaller RNA. they will also have same specific charge)
The properties of stationary phase  is very important in controlling the separation process. Without knowing what resin is used, it will be difficult to comment about why RNA is not retained.
Sometimes the strong basicity of the stationary phase, such as in quaternary ammonium resins, degrades RNA by alkaline hydrolysis.
If yours is a commercial resin then you will have a tough time finding out what exactly it is made of. Unless of course you break the column open and do a molecular analysis of the resin :P


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Source of DNA sequences
I'm working on a project where I am taking DNA sequences and translating the codons into musical notes. I have some good ideas of how to do this, I'm just not sure what sequences to work with. My case study and a lot of my initial research showed that anything larger than a protein is too much to work with for now.
So my question. Where can I find protein DNA sequences in some standard format. I've looked at NCBI but I have no idea what I'm looking at or if I'm downloading the right stuff. Is there a link that I can go to that will have a listing of a bunch of difference protein sequences that I can download?

Huh, interesting idea. Might be a good way to flesh out some patterns, since humans are better at hearing patterns in music than seeing them in abstract symbols.

I just noticed the question is from 2 years ago. Are the results of your work available somewhere online?

GenBank and RefSeq have a huge collection of DNA sequences that can be downloaded in Fasta format. GenBank makes it very easy to search for sequences (for example, using the organism name) but will often have redundant data and varied types (everything from whole chromosome sequences to mRNAs to gene sequences to ESTs). RefSeq has much cleaner, non-redundant data but might take a little more effort for you to find the sequences you want. Depending on whether this has any effect on your project, you might want to consider that. On the RefSeq page, under the FTP menu you can click Genomes to see which genomes have RefSeq data available. The Fasta sequences for a particular genome will be stored in a dedicated directory, possibly subdivided into further directories by chromosome. What you want are the Fasta files (ending in .fa, .fasta, .ffn, or something like that), keeping in mind they may be compressed (.fa.gz, fasta.gz, etc).
Alternatively, if you already have a specific organism in mind, then you could do a Google search to see if the genome for that organism has been sequenced. If so, there is almost always a dedicated website where you can download DNA sequences for that genome.

I've been to those sites, I just don't know where to go to get a list of sequences. I want a wide variety of sequences so a list or the root of a directory would help the most. I'm not looking for a specific sequences. I just need a lot of them.

In GenBank for example, if you search for Vitis vinifera, you get 131k reults. If you click the "Send to" button, select file, and then Fasta format, it will allow you to download a Fasta file with the sequences. If that's not what you're looking for, you're going to have to provide a little bit more detail before we can help you.

I don't know a lot about biology. I'm researching different ways to encode data to help with perception of the data. So I know alot about information, just not DNA. I need a bunch of sequences to use as tests on my DNA to music tool.

Is 131k sequences enough?

Ok this is a good answer I did what you said and have exactly what I wanted, actually a little better now that I see I can search specific organisms.

A standard format would be the FASTA format.
If you have a few proteins of interest that you would like to look at you can simply select 'Nucleotide' at the top of the NCBI page, enter your protein's name and then press the FASTA button below each result you are interested in.
If you just need a large dataset of DNA sequences that code for proteins you could for example use the 'nt' blast database.
(I believe this is only protein sequences not entirely sure though, I thought it would be easier to get)

I've seen that format too, is there a place I can go and download a lot of sequences in that format?

good answer. I'll download the 10 gb file and get to work haha. Thanks

Since I can only add comments here: I agree with Daniel Standage that Genbank is the more suitable ressource but how do you ensure there that it's only protein coding DNA? You could limit your search for mRNA on the right which should throw out some non-protein results however then you have mRNA sequences which of course differ from the DNA sequence they originate from. If that is not an issue I'd say go for that.

This suggestion helped a lot

This is more of a comment, but too long to put in a comment box, so I'm putting it here.
This is a fun idea you're doing. I have a half baked idea (assuming you're looking for input) if you want to explore it further -- or not ... by the time I finish writing this, I might realize it's too silly, but still ... let's see.
It might be fun to take the sequence of two organisms, let's say mouse and human and align certain regions to each other -- imagine this is like playing a piano where the "left hand" might be the mouse sequence, and the "right hand" is human.
So, say you take a gene that are shared in both, like CCND1. You can align them against each other and you'll find large portions of the sequences are common (with some mismatches, obviously). In these regions, the left and right hands are playing together (different octaves.
You'll also find gaps in the alignments where you'll have a stretch of "mouse only" or "human only" sequence, and in these regions the left or right hand play alone (solo).
For instance, say the two alignments look like this:
mouse: CGTGGGAGGCTCTTGAGCCTGGAAACACTATCGCAGTTTGTACGGAATGCACTTGTTCTTTACAAAAGG
human: CTTGGGCGACA---GAGC---GAGACTTTGTCTCAAAAAAGAAG--------------------AAAAG

In this case, you see stretches of the alignments where the mouse (left hand) will be playing a solo, and other times the two hands play in "harmony."

The tool I'm making can be used to do this without any modification. Cool idea though. I may make a blog for it once I finish the hard parts and post it to this QA just for reference.

Here's the tool http://dnasongs.brandonhamric.com. The alignment part is left out because of some bugs in playing multiple parts at once, but oh well.


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Does bioluminescence occur in humans too?
I read that Japanese researchers have developed very sensitive camera that recorded bioluminescence in humans; is it possible and if so what is the mechanism behind it?

I assume blackbody radiation doesn't count?

We have more bacterial cells than eukaryotic cells in our bodies, so maybe some of them are bioluminescent?

From the article you linked:

virtually all living organisms emit extremely weak light, spontaneously without external photoexcitation. This biophoton emission is categorized in different phenomena of light emission from bioluminescence, and is believed to be a by-product of biochemical reactions in which excited molecules are produced from bioenergetic processes that involves active oxygen species

They reference these two works. The first is a 1988 review from Popp et al. (1988):
Biophoton emission - Experientia 44:543–600. (sorry, I cannot find the link to a full text...)
Fritz-Albert Popp is the biophysicist who first developed the biophoton theory.
The second work they reference is by the same first author:
In vivo imaging of spontaneous ultraweak photon emission from a rat's brain correlated with cerebral energy metabolism and oxidative stress. - Kobayashi M, et al.
Finally, a search in Pubmed reveals various other articles by different authors studying different species.


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Can methylation from DNA get copied to RNA during transcription?
Methylation on gene-body and 3'UTRs if copied to mRNA can potentially regulate post-transcription modifications or expression regulation. But I'm not sure if they are maintained after transcription or if they get all de-novo methylation.

I don't believe anything should change in the majority of DNA->RNA transcription. DNA methylation typically occurs on the non-watson crick side of Cytosine so it shouldn't affect the base-pairing.
However, there are a few hypothetical situations that would result in alterations of the transcribed RNA. The sponatneous deamination of the 4' amine would convert the base into uracil. If there is an additional 5' methyl, the 5-methyluracil would be recognized as Thymine.
(edit) I've talked with several genomics folks about this topic and it turns out that M5Cytosine is very resistant to deamination due to the presence of the Methyl group. As a result, the instance that I have just described is actually very rare.

5mCytosine to Thymine deamination
The other situation would be to errors in DNA proofreading. Does the 5mCytosine affect the fidelity of RNA polymerase? I honestly don't know but it would be worth examining.

Is there any citation of altering cytosine on RNA to 5mC?

@Garima Kushwaha. Does this count? http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2836557/

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC307917/ This paper has the opposite view; that the rate of deamination is higher in the methyl version which accounts for its increased mutation rate.

There is an article in PNAS Conservation and divergence in eukaryotic DNA methylation who used:

next-generation sequencing to investigate the DNA methylation patterns
  in eight divergent species, including green algae, flowering plants,
  insects, and vertebrates. Their data allowed a comprehensive
  comparison of whole-genome methylation profiles across the plant and
  animal kingdoms, revealing both conserved and divergent features of
  DNA methylation in eukaryotes.

So there is some conservation.

That evolutionary conservation seems very interesting, but the question is whether it is maintained somehow into the transcribed RNA


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Why is the 3'UTR region highly methylated in most of the human genes?
Most of the human genes are found to be highly methylated in their 3'UTR region (0.8-0.9%). I was wondering if there is any specific reason for this?

any reference? would be interested to see it...

According to Choi et al. Genome Biology 2009, 10:R89, DNA methylation at both coding boundaries may regulate transcription elongation and stabilize splicing by reducing the occurrences of exon skipping.
From the abstract:

Here we report a genome-wide observation of distinct peaks of
  nucleosomes and methylation at both ends of a protein coding unit.
  Elongating polymerases tend to pause near both coding ends immediately
  upstream of the epigenetic peaks, causing a significant reduction in
  elongation efficiency. Conserved features in underlying protein coding
  sequences seem to dictate their evolutionary conservation across
  multiple species. The nucleosomal and methylation marks are commonly
  associated with high sequence-encoded DNA-bending propensity but
  differentially with CpG density. As the gene grows longer, the
  epigenetic codes seem to be shifted from variable inner sequences
  toward boundary regions, rendering the peaks more prominent in higher
  organisms.

Their data (figures 1 and S2), however, do not support a generalized increase in the 3' UTR regions in either human T cells, mouse liver, yeast or flies.

Thank you so much. This paper looks very interesting. I will read it and see if I have more to discuss.


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Fetal development, gastrulation and embryonic disc
I am completely confused by the images circulating on the internet of human gastrulation.
First, lets see how it happens in deuterostomes. This image depicts the process:

(image is from Wikipedia)
From here we can conclude that blastula becomes gastrula when some of the ectoderm beecomes endoderm, the place where it goes inside becomes anus and then mesoderm is formed.
Ectoderm here is the outermost level and gastrula already has anus.
However, in this image of human gastrulatuion we see completely different things:

(image source)
The mesoderm here is the outermost layer, ectoderm is inside and the gut cavity is formed by the separation of a part of the yolk sac. There is no anus and the posterior end of the gut is blind. Also other similar images suggest that a twins may be separated already after the mesoderm was formed (thus uniplacental twins).
The lack of agreement between the images disturbs me.
Just to point out some of the differences in the depicted processes:

In first image mesoderm forms after gastrulation, on the second it forms far before gastrulation
In the first image anus forms in the process of gastrulation, in the second image anus remains blind
In the first image ectoderm is the outermost layer, while in the second picture mesodem is the outermost level that encloses all, including ectoderm.

Two suggestions: Please link to the source of the images, and please state what your actual question is.

Human embryogenesis is much more complicated than the more general and simplified picture given in your 1st figure.
For details, please study http://en.wikipedia.org/wiki/Human_embryogenesis
To point out the most distinctive features which might have led to your confusion:

Before gastrulation, the blastocyst cavity is formed.
Only the inner cell mass undergoes gastrulation.
Mesoderm forms quiet late and spreads, thereby also forming the chorion as well as the amnion.
The embryo itself is formed from a subset of all embryogenetic cells. This is shown in your 2nd figure, part C and D. Yet, tissues are still going to spread such that the final ectoderm as well as mouth and anus will be formed.

The second picture does not show human gastrulation.
Your source talks about the development of yolk sac in human embryos, and does not claim it depicts gastrulation. In human embryos gastrulation happens about 7 days after fertilization and the development of membranes, as depicted in your second picture, begins about 15 days after fertilization.
I highly recommend the part of Chapter 11 from "The Developmental Biology", which deals with early mammal embryo development, from fertilization till formation of the body axes.

How it turns that mesoderm is the outermost layer in the second picture and not in the first one?

Second picture doesn't mention mesoderm. Look closely at the titles. It's just that colour schemes are different, so one thing is blue in the first one and another in the second one.

Mesoderm is red on the second picture. It is tissue that forms heart.

Also ectoderm and endoderm are shown in direct connect to each other in the second picture while on the first one they are separated with mesoderm

The Wikipedia protostome vs. deuterostome figure depicts a "prototype" deuterostome, such as an echinoderm or an amphibian.
In amniotes (reptiles and their descendants - birds and mammals), the giant amniotic egg full of yolk led to profound changes in early embryogenesis, including the disappearance of the true blastopore. (Its analogue as organizer of gastrulation is the Hensen's node, but it is dorsal and does not form the anus.) Placental mammals have secondarily lost the amniotic egg, but a substantial part of their gastrulation movements still reflect its former presence.
Although in us the blastopore does not form the anus and does not even exist, we are still classified as deuterostomes because of our clear kinship with amphibians.

This gives a third theory - that the proto-anus is homologous to neural tube!

By your theory how neural tube is formed in amphibians then if they have blastopore which becomes anus?

What is the question?


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What is the species of these mushrooms?
The mushrooms are gilled with a light-brown cap. The stem is widened to the base.
What species is it? Is it considered edible?
They are found in mixed forest in Moscow, Russia. They grow in the ground quite separated from each other.

Looks like Boletus edulis. If that is the case is not only edible but extremely yummy. However, please do not trust me too much on this, I am no mushroom expert.

@nico it cannot be boletus because it is gilled, while boletus is pored.

Please, describe where have you found them (geographic location, type of habitat). This kind of information is very useful for species identification.

@Anixx: told you not to trust me on that :P

@Marta Cz-C done

This is Clitocybe Nebularis, an edible species.

I had a quick look in my books (for the British Isles and Europe) but although I found a couple of candidates I don't feel confident in either identification.
I suggest that you have a look at Roger Phillips' online identification guide  - this will suggest a few identification criteria that you haven't considered in your question.

"No results found. We were unable to find a match for your search."

For the record, my two candidates were False Death Cap (immature specimens) and St. George's Mushroom (but this is a spring fruiting species). These were based on the general colour and swollen stem base only.

@Alan Boyd the cap is smooth and there is no veil at the basement. Also there is no skirt. Very far from False Death Cap.

@Alan Boyd My candidates are species of Cortinarius genus (Cortinarius glaucopus http://for-grib.ru/IMAGES/pautinnik-sizonozhkovyjj-cortinarius-glaucopus-lllo5b.jpeg Cortinarius praestans http://www.aranzadi-zientziak.org/fileadmin/images/micologia/Eskaneatuak/09_digital/cortinarius_praestans_paa_091103.jpg Cortinarius esculentus http://infofishing.ru/uploads/posts/2011-12/1322998170_pautinnik.jpg ), Tricholoma portentosum http://www.dipbot.unict.it/funghi_etna/photogallery/Tricholoma%20portentosum.jpg Clytocybe nebularis http://nepoganki.narod.ru/Photos/074_photo.jpg

http://farm6.staticflickr.com/5190/5602239343_08378ce877_m.jpg

Or Clitocybe clavipes http://mycoweb.narod.ru/fungi/Submitted/SJG2/Clitocybe_clavipes_JS20040829_med.jpg

It turned out to be young Clitocybe Nebularis, an edible and tasty mushroom.


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Do hormone drugs affect whether a person feels sexual attraction to males or females?
I know that ingesting testosterone and other hormonal drugs may stimulate libido and increase sexual desire.
But I wonder, if a man ingests female hormones such as estrogen, will he experience sexual desire towards other men or not?
Similarly, the other way around, whether a female ingesting male sexual hormones will experience desire towards other women?
The question is motivated by the interest to know whether transgender people, particularly, the MtF transsexuals engaged in prostitution experience genuine attraction to males.

Testosterone injections do not increase libido in healthy adult men: http://www.eurekalert.org/pub_releases/2001-11/aps-tdr113001.php (at least not more than a placebo)

@dtech what about teenagers? It is often said that they want more sex because of hormonal boom.

There is no evidence that postnatal hormone exposure can change the sexual sexual preference of an individual. However atypical hormonal stimulation of the fetus can induce homosexuality.
Homosexuality does not develop without a variety of social factors which are up-to-date mostly unexplained. But can develop without hormonal stimulation.
As real life examples there are a androgen antagonists for the treatment of of prostate cancer, which reduce the testosterone level in males. Under treatment the men often turn softer and more emotional, as described by their wifes. And there is beer which contains oestrogens and can induce the growth of female breasts in men. But none of this mechanisms has been observed to turn males homosexual.

Further Reading (second text is free fulltext):
[1] http://www.ncbi.nlm.nih.gov/pubmed/23397798
[2] http://endo.endojournals.org/content/152/8/2937.long

People suspect that hormones for have an effect, but there are also genetic and biological factors. Hormones have caused some animals, such as frogs, to change sexes. Also, both genders have testosterone and estrogen in their bodies. Men just have more testosterone and women have more estrogen.

Can you expand on that, possibly putting some references? For instance, although it is true that the balance T/E2 is higher in men, but testosterone, in men also act (especially in the brain) after being aromatized to estrogen and local concentrations can be very high.

Suppression of testosterone activity is correlated with lowered sexual desire in both men and women...


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What is this insect looking like a wasp or an ant?
It looks like a black wasp or big ant with wings. It produces no noise. It mostly sits at one place on the wall, does not move. The young (or another gender) form has unproportionally long back legs, making it look like a spider.
It has big head with big eyes.

Please include the size, location and weather details

These look like flies to me, but I'm not going to go any further than that.  Hopefully someone with more knowledge (and some idea of the location of these images..) will be able to get more specific.

To me they look like wasps.

These are two different kind of insects:
First insect
There is one pair of translucent wings (admittedly, the number of wing pairs is not visible from the photo), what tells us it must be some kind of fly (Diptera).
Further, the antenna is rather short, from what we can deduce it must be a brachyceran fly.
Even further, it has three segments, so we can conclude it is a member of the family "soldier flies" (Stratiomyidae).
A friend (a dipterologist), upon seeing the photo, immediately argued it must be a "black soldier fly (Hermetia illucens), a meanwhile cosmopolitan species that has gained economic importance in organic recycling.

Second insect
This one is much trickier, I think.
It does look like a shore bug (Saldidae): the large eyes, slender and long antenna and legs, the flat and oval body - everything fits.
But shore bugs are tightly bound to their habitats (shores of all kinds of waterbodies). And at least in Europe, it is very unlikely (although not impossible) to find one inside a building.
Also, shore bugs are very agile and are fast runners, jumpers and flyers - what contradicts the OP's description ("It mostly sits [...], does not move").

I have also seet a variant of the first insect but much bigger (about 1.5x).

This is a holometabolous insect, meaning with a complete metamorphosis. Therefore the second picture is not a young, a young would be a larva or a nymph, i.e., it would look nothing like a smaller version of an adult.
The insect on the second picture, if it is indeed the same species, is likely the male.

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


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Is there any species of mammals where males can feed the offspring with milk?
It seems to me that an evolutionary path where not only females, but also males could feed the offsprings is entirely plausible: the males anyway have niples, so it is easy for the offsprings to confuse them for female nipples, and depending on hormonal background, some males are even capable to produce fluids with milk glands (even some humans). So, such capacity in males theoretically could improve survival chance. Also, this would somewhat relieve the females who contribute a lot of resources to the offsprings during pregnancy while the males in some species do essentially nothing except insemenation and/or fighting between themselves, thus wasting resources.
Given these speculations, if there is no such species with this trait, what is explanation for this?

It's not easy to give a definitive answer ("...what is explanation for this?") for a reason something doesn't exist. Why don't we have 31% O2 in the atmosphere instead of 21? What's the reason twins don't occur more often than they do? Since flight is a good escape tactic, why did only one mammal develop true flight? The number of such questions are endless. The reason is, it is what is (evolution.)

Does this answer your question? Why do some bad traits evolve, and good ones don't?

In the large fruit-eating bats Dyacopterus spadiceus and Pteropus capistratus the males are known to lactate. Wikipedia has an article on male lactation which mentions these species.  However, as discussed in an article by Kunz and Hosken (1), it is unclear why the males of these species lactate.  The biology and normal life history of these species is not well known, and apparently there are no reports of males actually suckling young bats.  Kunz and Hosken discuss ways in which the male lactation in these bats might be adaptive even if no or little nutrition is provided to the young by the male.
(1): Kunz, T.H. and Hosken, D.J., 2009. Male lactation: why, why not and is it care?. Trends in Ecology & Evolution, 24(2), pp.80-85; [PDF]

As @mgkrebbs mentioned in their answer, Dyacopterus spadiceus and Pteropus capistratus are the males speciees known to lactate. The Wikipedia link also mentions one more species - goats (Gómez et.al., 1999). In fact, male lactation has been observed in a few domesticated animals, including cats and guinea pigs but on rare occasion though it's not yet clear what is the mechanism to produce milk..
Moreover, Jennifer A Brunton and Thomas H Kunz of Boston University and their colleagues who studied the fruit bats in the Krau Game Reserve in Malaysia, suspect that the mammary glands of these bats contain an enzyme that converts testosterone into oestrogen -- a hormone that excites milk secretion. (source)

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


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From which ancestor species did humans inherit orgasm?
From what ancestors did humans inherit orgasm?
Do fish experience orgasm?
Are the male and female orgasm the homologues that can be traced to the time when there was no difference in sex between individuals (as in fish) or developed independently?

You're going to have to clarify. What do you mean by 'orgasm'? Do you include the pleasure, or just the act of ejaculation?

-1 using the term "Invented" makes this question nonsensical.

The meaning is completely distorted. I was asking about human ancestors, namely, fish, not "asexual species".

@nico I consider you vandalized the question. My main question was wehether female and male orgasms are homologues but you removed that part.

@Anixx: I did leave a comment exactly for that reason. Your last sentence does not really make much sense in English. By the way you wrote: to the time when there was no difference in sex between individuals. I don't read that as fish (and I did leave the fish part in my edit).

@nico fish exhibit androginous behavior with the same individual follows through male and female stages.

@Anixx: then you should rephrase it, because your sentence does not mean that. Fish DO have a sex, they do reproduce sexually and there are differences between male fish and female fish.

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.


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What species is this? What the fruit?

The berries of the fruit are sweet. The tree is growing in Israel.

Please edit your post to include where this tree was growing  — for identification questions it is important (and often essential) that you include location information.  Pictures of the bark could also be helpful.

@tyersome I added bark

This does look somewhat similar to a mulberry though I agree it doesn't look right for a white mulberry.  I would, however, guess that it is something in the Moraceae (Mulberry family). —— To test this you could break a small branch or tear a leaf — plants in this family produce latex (a milky looking sap) when damaged.

@tyersome after thinking about this, I agree.

Is this a street/landscape tree?  What town?  Jerusalem has a detailed tree inventory if you read Hebrew.

@Bryan Hanson yes it is street (planted) tree in a park. It is in Haifa.

Unfortunately I can't locate a street tree inventory for Haifa.  And street trees are frequently not native, which expands the range of possibilities. Your pictures are great, someone will surely know this tree but I cannot figure it out.

@tyersome I tested for white sap and there was none.

Well that's confusing!  Maybe Haifa has an urban forestry department (or something similar) that might have someone who can answer this?  If you do get an answer, please share it here.

Looks like it is Phytolacca dioica.  I found this by searching your first image in a phone app called Pl@ntNet (PlantNet).  Looking at Wikipedia confirms the ID.
Interestingly, you said the fruit was sweet.  The North American relative Phytolacca americana is extremely poisonous.  A brief search suggests your species is possibly poisonous, with reports about the leaves more common than the fruit.

This site says the berries are juicy so can reduce thristyness: http://travelermap.ru/chudesa-prirody-13/

Good to know!  Another interesting difference is that your specimen's berries are yellow-green, while P. americana has intensely red-purple berries, due to betalain pigments.  Glad we figured this one out!

Phytolacca esculenta also has black berries but it is edible and cultivated. The difference between this and american variety is the form of the berries. Also, dioica is a tree while the other two are not.

Perhaps a white mulberry? See the Wikipedia: https://en.wikipedia.org/wiki/Morus_alba

Of course, not. The berries are of totally different size and the leaves are totally different.


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Besides fruits and milk, what other things in nature are "intended" to be eaten?
Besides fruits and milk, what other examples are there in nature where it is beneficial for a species to have some part of its biomass eaten by others so that it evolved to produce nutritious parts to be eaten by other organisms? For example, plants having animals eat their fruits as a means of transporting their seeds.
Update.
I think there are at least two philosophically different scenarios that interest me.
One is when the substance is intended to be eaten by the same species (example: milk).
The other is when it is intended to be eaten by another species (example: fruits).

I agree with @Arnb below, this is not a bad question. Will edit to clarify.

Thanks to @Roland's edit the question now makes sense. It is an interesting question. I am removing my close vote, my now obsolete comment and +1

Difficult to define "intended" seeing as there is no intent in evolution - lactation provides for offspring, fruit is taking advantage of heterospecifics to spread seed, nectar is an incentive which makes animals aid pollination, all photosynthetic plants convert sunlight to edible energy but is it "intended" for using within the plant or could it be an evolutionary precursor to "intent" to feed conspecifics and heterospecifics?

Let's say intent means both the food stuff and the interaction evolved by selection with benefits in both species. Did evolution intend for fruit production? Maybe the fruit around the seed was a good way to provide a nutrient rich early environment, or helps the seed float in water to spread it, and then animals came along and started eating them

This is similar to an egg, the egg provides a nutrient rich environment for the chick to grow, humans (and other species) came along and started eating them.

@rg255 well nutrient storages are not quite intended to be eaten. Otherwise, nuts or potatoes or body fat should be counted.

@Remi.b seems it is closed now.

There are plenty of examples! Here is a short list

Defence ("Eat that so that you don't eat this")

Evisceration. It is the ejection of internal organs so that predator eat them but not the prey entirely. (sea cucumber does evisceration)
Lizard's tail being fragile on purpose

Parental care

Milk
Regurgitation
Sexual Cannibalism (as it is often hypothesized as benefiting the male also as he indirectly nourish his offspring)
In haplo-diplontic species, one of the two generation can be much bigger and can transfer its nutrient to the other generation (offspring), such as in moss for example.

Mutualism

Nectar
Fruits
Honeydew produced by aphids to attract ants which protect them from predators
Ant breeding fungi

Symbiosis

Lichen
Root nodule

Social behaviour

Honeypot ant (if we are happy to consider the honey stored in the ant for a long being part of the ant biomass).

Human related

The researcher in parasitology that feed his mosquitoes with his own blood!
Crops (and other things) under artificial selection. It is here just cases of mutualism where humans is involved.

Another point which you may incorporate: Plants also produce another kind of nectar (extrafloral nectar) to attract ants and other insects which protect them (plants) from herbivores.

I don't think evisceration of sea cucumbers is actually intended to feed and satisfy the predators (as per wikipedia). It is for trapping and immobilizing them.

I did not use the word "biomass" in the original question.

Please don't editorialize in your answers. If you want to respond to a particular member or comment, use a comment. Otherwise, use [meta]. That's what it's there for. I realize we were just discussing this, but at this point there are two answers (one is mine) against your point of view with a total of 7 upvotes, and one answer (your own) which has been downvoted (disagreed with) once. If you want to speak critically about the post, please use comments like everyone else. I won't downvote your post this time, but it's an option in the future.

@MattDMo I removed the section 'Semantic issue in the post'. I really find this refusal of any discussion of semantic in answer silly but it looks like the majority of user like it this way, so I will just comply to the majority. Thanks for the comment then! Without this section, it will be likely to have discussion in comments of the kind as those we have underneath Arnb answer though. Btw, I upvoted your comment by mistake :)

I found this question very interesting. Let me explain. In the course of evolution, all organism developed properties (may be structural, functional or other) to protect themselves from predators. It may be by mimicry or development of some defensive or offensive methods. There are only a few exceptions to that - where the organism allows other organisms to eat its body parts. In the question the "intended to be eaten" indicates this. With this sacrifice surely the organism gets some survival advantages of itself or its children. Fruit and milk are among these rare examples.
Another example should be nectar of flowers. Plants make nectar so that bees visit flowers to drink it and unknowingly spread the pollen.
There should be other examples also.
Please note the tag "evolution".

So, one seemingly should add honey, anything else?

What about mushrooms?

@Anixx  nectar, not honey.  Honey is produced by bees as food storage for their colony, and they certainly are not intent on giving it away to other species. Hence all the angry buzzing when beekeepers harvest their hives.

Please don't editorialize in your answers. If you want to respond to a particular member or comment, use a comment. Otherwise, use [meta]. That's what it's there for.

There are only a few except to that where the organism allows other organisms to eat its body parts. This is complete anthropomorphism. A plant doesn't "allow" other creatures to eat its body parts - it either evolves a defensive mechanism against a particular class of creatures, or it doesn't. It "decides" nothing. Some plants are toxic for some creatures and perfectly safe for others, or have some toxic parts and not others (take rhubarb as an example). Did the plant make a choice to do that? Of course not. It just happened.

I used first person in my answer for the sake of simplicity. Otherwise I had to say "in the process of evolution the plants with their seeds covered with edible fruits got naturally selected with respect to other non-fruit-bearing plants of same hierarchical category. The primary purpose of the fruit is its edibility. In other words fruits are evolutionarily selected  to get eaten. " To avoid this long and complex sentence I used terms such as " allows" in my answer. I didn't use "decide" in my answer. So MattDMo please keep it out of quotation marks.

Comments are not for extended discussion; this conversation has been moved to chat.

In many species (crickets, salamanders, newts, arachnids, moths) males provide a nuptial gift in the form of a spermatophore which aids the female if consumed (normally via additional nutrition, but in some species the package may contain toxins that make the female less susceptible to predation).
Also, @Arnd mentions nectar in the context of encouraging fertilisation but extrafloral nectaries are believed to have evolved specifically to produce nectar for consumption, in this case by insects that will attack herbivores and thereby indirectly protect the plant.
You could make a case that bitter or toxic secretions that are intended to discourage predation have evolved specifically to be consumed, but I suspect that's not really the way this question was intended.

"You could make a case that bitter or toxic secretions that are intended to discourage predation have evolved specifically to be consumed, but I suspect that's not really the way this question was intended." - yes!

I think cannibalism in caterpillars is an example. Especially the larvae of the Lyceanidae, but also anthocharis cardamines are canniballistic. The caterpillars often find themselves on a plant that is too small to sustain more than one of them. Cannibalism is then beneficial to the species, because one butterfly is better then ten starved larvae.
As cannibalism also makes the caterpillars grow faster, it could (hypothesis, not proven afaik) be a survival strategy (or semantically more correct: trait).


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Is tactile perception two-dimensional or three-dimensional?
Is tactile perception two-dimensional or three-dimensional? Can tactile sense be mapped on 2-dimensional map of the surface of the human body or does human receive tactile signal as a 3D position (owing that internal organs can also feel pain)?

It's not 2D: Tactile perception can very simply understand a ring around your finger. If you projected the skin of your body onto a 2D plane there would be a way to represent this sensation, but only as an irregular shape. So you need a third dimension to cognitively process this sensation.
But Phantom pain tells us the brain doesn't always register tactile perception from a true 3D mapping. For example a person without an arm could feel pain in a finger that doesn't exist. Not always, but sometimes.
So it's greater than two, and sometimes three doesn't fully describe the known phenomena. Therefore it's (at least) 4-D.

Hmmm I don't get how phantom pain affects the number of dimensions.

Well, vision is 2D * 2 (two retinae) but visual perception is 3D, auditory signal is 1D * 2 (two ears), but its perception is 3D. The 3D perception in these senses are results of analysis of the lower dimensional sensory signal combined with various other internal states. (Internal states can integrate information over time to produce better percepts.)
Likewise, each tactile sensor is a point source, but the percept of the total tactile sensory stimuli is 3D; I can tell where the source of the sense is in 3D space relative to my body position. The signals will have to be combined with the proprioception and state information in the brain to do so.
Note that these 3D percepts don't always work perfectly. Sometimes we form the wrong percept or fail to get a percept.

Sorry, but you cannot hear in 3D using 2 ears in any case. It is mathematically impossible.

@Anixx but you can. Head transfer function and prior knowledge. It's mathematically possible, although not always the case.

@Anixx https://en.wikipedia.org/wiki/Vertical_sound_localization combined with other cues, not perfectly, but possible.


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Is it possible that there are unknown vitamins?
Is it possible that there are vitamins or other essential nutrients about which we still do not know?

This question is tending to be POB. There is always a possibility that we don't know the mechanism of every enzyme. You should add some rationale behind your question so that it becomes useful to everyone. A point to note is that if someone acquires a mutation which prevents the formation of a metabolite that humans can normally produce then they would need it in the diet.

@WYSIWYG — Which one of the 39 possibilities for the acronym POB had you in mind? But I agree. I would think most "Is X possible" questions are matters of opinion and off topic. They assume that X currently does not exist/happen/has been observed, so unless your attitude is that all things are possible, the answer has to be a matter of opinion. And, indeed, such questions are can only rarely be "practical, answerable questions based on actual problems that (people) face.".

Yes, it is possible that there is a vitamin or other essential nutrient that has not been identified so far.
Essential nutrient means any substance normally consumed as a constituent of food which is needed for growth and development and/or the maintenance of life and which cannot be synthesized in adequate amounts by the body (fao.org). Essential nutrients include vitamins and some minerals, fatty and amino acids.
Choline: An Essential Nutrient for Public Health (PubMed, 2009):

Choline was officially recognized as an essential nutrient by the
  Institute of Medicine (IOM) in 1998.

The fact that choline has been recognized an essential nutrient relatively late suggests that there may be other nutrients that are not recognized as essential today but may be in the future, for example:

Aluminum (Biocyclopedia)
Boron (PubMed)
Nickel (WebMD)
Silicon (PubMed)
Vanadium (PubMed)

Please not that term Vitamin excludes essential minerals, fatty acids or amino acids. So the other examples you listed - even if considered essential - would unlike Choline never be a vitamin.

I'm not sure if I understand your comment. Essential nutrients include vitamins, some minerals and some amino and fatty acids.

Thats correct of course, I was mostly going from the fact that the OP used the word vitamin the title but then used "essential food components" in the body text. Maybe adding a short comment about the distinction might improve the answer.

Russian wikipedia says choline is vitamin B4 (since the 1930s) and in modern view is not a vitamin.

@Anixx, I'm not saying choline is a vitamin, but it is sometimes described as a vitamin-like substance. The source I provided in my answer and Office of Dietary Supplements by National Institute of Health in the US, among other say choline is essential.

https://iubmb.onlinelibrary.wiley.com/doi/pdf/10.1080/15216540500078939 says vitamin B4 can refer to many things


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Can we artificially produce a species that would be able to live on Antarctic ice sheet?
Can we artificially produce a multicellular species that would be able to live on Antarctic ice sheet?
By means of genetic engineering, selection etc.
UPDATE
There are organisms, called Watermelon snow or, scientifically Chlamydomonas nivalis, which do exactly that: populate snow. They are not multi-cellular, but eukaryotic (not bacterial), photosynthetic and form extensive colonies. They already populate both Arctica and Antarctica. They prefer snow to ice.

Some bacteria manage to live there, besides the arctic cold that kills most of the other animals.... So, you mean to create an organisation, from that kind of bacteria, or just a colony of some monocytes?

There's plenty of wildlife in Antartica already (wiki > wildlife of Antartica)

I know this is closed, but I just want to mention one of my favourite papers: https://www.nature.com/nature/journal/v310/n5974/abs/310225a0.html :)


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Convergent evolution of fruits
Many fruits are not homologous, originating from different parts of a plant. Yet they all have similar properties:

Ripe fruits all have yellow to dark red color
They all have a lot of water and sugars, even in dry climate where water is in shortage.
Besides sugars they usually have acids making them sour to sweet in taste

I understand that these possibly developed as a contract between the plants and the animals in that the plant would provide beneficial fruit tissue so that the animal to swallow the seed so to propagate it for longer distances.
But I wonder, why there are no fruits that would imitate the taste of meat, nuts, seeds,  foliage, grass, mushrooms, roots, milk and other food sources, common for the animals?
Why there are no salty fruits for instance or those rich in proteins rather than sugar and water, or having the smell of carrion?

I appreciate the intent of your question but I suggest you think more broadly about what are fruits. Coconuts are fruits. Dandelions produce fruits. Durian fruit smells terrible to most people. Look at samaras. Any seed-bearing structure on flowering plants is a fruit.

@3cat under fruits I explicitely mean those tissues intended to be eaten by animals. I am not interested in the other varieties. I ate durian, and as it was fresh I did not notice any distractiong smell. Do you claim it is not intended to be eaten? What's the purpose of it then?

Howe and Smallwood (1982) provide a nice review of the many methods of seed dispersal that have evolved in plants. The review is broad but they do have a section on frugivory.  They highlight hypotheses developed by McKey, and Howe and Estabrook (see Howe and Smallwood for citations) that suggest plants may use one of two strategies.
One strategy is the "high investment model." Plants invest lots of resources to produce large seeds and nutrient rich fruits. THe hypothesis is that these types of fruits tend to attract relatively few but specialized frugivores that are will to invest the energy necessary to find these types of fruits and their associated nutritional reward.
The second strategy is called the "low investment model." In this model, plants invest little in individuals seeds and fruits but produce an abundance of them. The hypothesis is that these types of fruits will be eaten by as many different potential seed dispersers as possible. These tend to be very small or starchy although they can still be colored as you describe.
Other factors also come into play. For example, tropical fruits tend to have large seeds and nutrient rich pulp while temperate fruits tend to be smaller and offer less nutritional reward.  All of this is placed in the context of the community diversity of frugivores. The Howe and Smallwood paper was an interesting read.
A paper by Gatier-Hion et al. (1985) looked at the characters of fruit choice and seed dispersal mechanisms by tropical forest vertebrates. The showed the relationships between fruit characteristics and the corresponding frugivores. They looked at 122 different fruit species and the frugivores that consumed them.  Their results showed that fruits tended to separate along one of three axes:

Heavy, indehiscent fruits with fibrous flesh and well protected
seeds vs light, dehiscent fruits with unprotected seeds. Many of
small fruits are red,
Lots of seeds produced (typically the the large indehiscent) vs few
seeds produced, and
Juicy and brightly colored fruits vs dry and dull-colored fruits.

Figure 2 from Gautier-Hion et al., shown here, shows the relationship between different frugivores and the fruit types.  Notice that small granivores, which are frugivores, don't eat large, juicy fruits. They consume lots of small green or brown grains that are easy to manipulate and produced in high quantities.  Squirrels are similar.

Thus, as you suspected, fruits and seeds have evolved in response to their frugivores but the fruits do not always have the traits you listed. I think, but do not know for certain, that the fruit traits you list are the result of selection being driving by the frugivores. The sugars provide lots of quick energy, which is necessary for active animals. The carbs probably provide a much greater nutritional reward than salts or proteins (which are present anyway). The colors may help the fruits to stand out against the green foliage (for organisms that are not red-green colorblind). These traits probably provide the greatest reward (lots of energy) with the lowest energy investment by the frugivore (easy to find).
Throughout, I've assumed natural conditions and not fruits modified by artificial selection for human consumption.
Literature Cited
Gautier-Hion, A., et al. 1985. Fruit characters as a basis of fruit choice and seed dispersal in a tropical forest vertebrate community. Oecologia 65: 324-337.
Howe, H.F. and J. Smallwood. 1982. Ecology of seed dispersal. Annual Reviews in Ecology and Systematics 13: 201-228.

Squirrels mostly eat nuts which are not intended to be eaten because their seeds are destructed in the process thus there is no surprise that nuts typically have no attractive color.

On the other hand, squirrels often take the nuts and bury them but do not later eat them. Dispersal from the plant's perspective has occurred.

How are you defining fruits? Because if you count any seed body of a flowering plant, you must include several items commonly described as vegetables, including pumpkins, zucchini, squash, cucumber, peppers, etc. And there are other colors of fruit, such as blue berries. These all serve similar functions for the plant, something eats the fruit, then deposits the seeds somewhere else.
If you define a fruit by what the average person calls fruit, then you've biased the population because humans have selected for juicy sweet tasting fruits over thousands of years of breeding. Humans like large sweet tasting fruits, so they selected for those traits, driving most fruits to have those traits. Wild fruits probably have much more diversity, and there would much less distinction between fruit and vegetable.

The most accurate way to define fruit is by using the botanical definition. Seeds are not fruits so nuts (in the sense of walnuts or nut mix that you buy at the store) are not fruits. Fruits are the seed-bearing part of the flowering plant.

I made an edit to remove the reference to nuts. By your definition many vegetables are still fruits.

Such as? Tomatos, widely perceived as vegetables, are fruits. Chili peppers (bell, jalapeno, habanero, etc.) are fruits. If it bears seeds, it is a fruit. Fruits, by botanical definition, bear seeds.

That's what I was getting at. I erroneously included nuts as fruits in my answer, and that reference is removed. Was trying to point out that fruits did not all go through the convergent evolution described in the question because not all fruits are sweet, many food items commonly considered vegetables are in fact fruits.

Cucumbers are green just because we eat not ripe cucumbers. Ripe cucumbers are yellow. Blue berries are just too dark red with a fungal film on the surface. I define fruits as the tissues intended by the plant to be eaten by the animals.


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What are some examples of scaling laws in biology?
I've seen that metabolic rate scales logarithmically as function of mass for many animals over an extremely large span of parameters. What other scaling laws exist at the individual level?

Here are some off the top of my head.

The height an animal can jump depends on the muscle cross-sectional area ($l^2$) and its mass ($l^3$). Mass grows faster with body size ($l$) so small animals can therefore jump higher relative to their body size ($l$) than large  animals. Very similar scaling exists for strength of limbs vs. mass, ability to fly vs. mass, etc.
In pinhole eyes (as found in clams and nautilus) sensitivity to light depends on the size of the pupil ($l^2$), the bigger the hole the more light gets in. However the ability to focus depends on the reciprocal of the size of the hole (but I don't know the scaling, so $l^{-n}$). Therefore there is a trade off between sensitivity and  ability to focus.
There are some recent models about foraging behaviour in a 2D terrestrial environment (with the front of the animal being a length  $l$) vs. foraging in a 3D marine environment (with the front of the animal being a surface $l^2$). The model predicts different behaviours for the size of prey animals should aim for.
The rate at which sound attenuates scales with the frequency of the sound as $1/f^2$. The frequency of a resonator scales with the reciprocal of volume $1/l^3$. So small animals make high pitched sounds which attenuate quickly and don't travel very far.
Finally, the properties of fluids change with size. The Reynolds number describes viscosity and is dependent on linear scale $l$. Therefore small animals experience fluids as viscous and can "crawl" through water whereas large animals have to "swim" through water.

However, any directly physical or chemical-physical property of biology will experience scaling laws.

This is great! Do you have any references for some of these so I can read more, especially the first three?

Are you looking for academic paper style references or something a bit softer? Here's a few papers anyway. Hope you don't get stuck with paywalls.
http://www.sciencedirect.com/science/article/pii/S0003347271801343 <- Bats calls
http://www.damtp.cam.ac.uk/user/gold/pdfs/purcell.pdf <- 70's paper about Reynolds
http://jeb.biologists.org/content/208/18/3581.full <- allometry of flight

Just for the record, jumping height depends also on the distance ($l$) along which a muscle's force delivers energy. The net result is independence ($l^0$) between jumping height and body size, but smaller animals still jump higher relative to size (by a factor of $1/l$).


text:
Is there a way to measure the amount of bytes that are possible to encode in a DNA molecule?
When I saw a DNA molecule for the first time, it kinda reminded me of a hard drive. It consists of slots and there are some possible combinations for each slot; in the hard drive these possible combinations would be 0's and 1's. In DNA, these slots would be G's, A's, T's, C's.
So, is there a way to measure the amount of bytes that are encoded in a DNA molecule?
I've made this question before in another forum, but the answerer provided me only with Shannon's theorem, which is $K=L-\frac{(1-q^L)^n}{q^L}$ and told me a little about genetic redundancy. I could only search for the ammount of slots which are present in the DNA, but this genetic redundancy thing got me stuck.

I am not sure what your question is - there are indeed four nucleotide bases in DNA, and these correspond to the "slots" you mention. You may want to have a look here: http://bitesizebio.com/articles/how-much-information-is-stored-in-the-human-genome/

This is the answer. I was just confused to the real ammount of data - because of the genetic redundancy.

You might find this thread over at skeptics interesting.

Unfortunately the answer is highly dependent on what you mean. In the simplest terms, comparing it directly to how we measure data storage in digital media, the number of different states of a DNA string of length $n$ can have is simply $4^n$. A byte holds $2^8$ different states so the number of bytes in a DNA string of length $n$ is $\frac{n}{4}$. Of course, actually accessing this information would be more difficult than simply having it in a strand of DNA.
DNA in real organisms is not random, however, so sequences are not randomly distributed meaning that you could compress that information down into less bits than that, Shannon information style.
However, you can decently argue that this doesn't really tell us how much information is in real DNA because real DNA has structure that matters. It has exons and introns and promoter regions and so on. Meanwhile, the sequences in protein coding regions are a lot more important than sequences in non-coding regions for the most part. Large parts of the genome are functionally irrelevant but because of this they tend to be more random and thus have higher Shannon information.

And then there was ENCODE's definition of function...

You might also be interested in this paper from EMBL-EBI about storing data on DNA.
Towards practical, high-capacity, low-maintenance information storage in synthesized DNA
They show they can get 757,051 bytes or a Shannon information 10 of 5.2 × 106 bits onto 153,335 strings of DNA, each comprising 117 nucleotides (nt).
George Church had a similar paper recently as well - Science


text:
How to compute properties of peptides ?
I have been tasked with writing a program for computing properties of a give set of peptides. These peptides are given as 1-letter amino acid sequences and I need to compute the following :

Length of peptide
Number of Each Amino Acid
Percent composition of each amino acid
Molecular weight
Net charge of peptide
Positive charge
Negative charge
Isoelectric point (pI)
Hydropathicity
Percent polar amino acids
Percent positive amino acids
Percent negative amino acids
Percent hydrophobic amino acids
Hydrophobicity
Lipophilicity
Amphiphilicity
Water-Octanol Partition Coefficient
Steric Bulk
Side chain bulk
Net donated hydrogen bonds
Percent \alpha helix
Percent random coil
Percent \beta sheet

While some of these properties are self explanatory ( eg. size, num. of amino acids, percentage of amino acids. ) and easy to compute. Other properties ( like Molecular weight, Net. charge, Positive charge, Hydorphobicity etc ) have been difficult for me.
I donot have Chemistry or Biology background and hence have found these difficult to compute. I would be appreciative if someone could point me in the correct direction ( I have already been through Wikipedia ) containing methods to compute the above mentioned properties or to a standard text which would explain the above mentioned properties and also provide methods to compute them. Thank you all.

Biopython and the other bio-programming languages typically have examples of how to do this kind of thing.
For example here is some python code for calculating some of these:
http://biopython.org/w/index.php?title=ProtParam&redirect=no
Many of the propensity scales are in this database:
http://www.genome.jp/aaindex/
And there are also biojava classes for accessing these. Essentially you will need to know what these physicochemical properties are and get access to a scale for converting the letter to a numerical value.

That's quite a laundry list, and I doubt someone is going to sit down and give you hints for all of them. Note that some of the properties (like percent alpha helix) rely on prediction method (secondary structure prediction, in this case). "Net donated hydrogen bonds" sounds like it makes sense only for a given complex with a solved 3D structure.
Nonetheless, you will probably find some of the stats implemented in EMBOSS, for example in the pepstats app.

Thank you for your reply. It has been helpful but would you happen to know of any reference text which goes over these properties ?

The introductory chapter of Proteins by Thomas Creighton (http://books.google.com/books/about/Proteins.html?id=hu8T_kI1LrkC) would be a great place to start. It was my Bible for introductory biochemistry in college!


text:
Does trypsin strip flask coating?
Mammalian cell/tissue cultures sometimes require flasks coated with proteins. My uneducated guess is that these proteins mimic the ECM, perhaps the basal lamina, so finicky contact-dependent cells can attach to it.
For instance, I have a BEAS-2B tracheal culture which requires a coating of albumin, fibronectin and type I collagen. This is applied by incubating an empty plastic dish or flask with a solution of these proteins overnight. I give this as an example of what a "coat" constitutes. You answer should be general enough to apply to at least the most common coat types, or if it depends on the coat, you should explain how.
Likewise, there is some variation in how the trypsinization occurs. To have a starting point, let's say I am trypsinizing according to typical ATCC recommendations: 5 minutes with 0.25% Trypsin-0.53 mM EDTA, then inactivate with equal volume medium. I haven't worked with a cell that can withstand this noticeably (but then I haven't worked with any exotic cells).
My question: When I trypsinize the cells to passage, what happens to the coat?
Since trypsin is a protease that cleaves even the attachment of cells to plastic, I am guessing that it will also destroy the coat. After the trypsin and cells are removed, the flask will have a tiny fraction of the protein coat that it had before, and will not support cells that require a coat any longer.
Am I correct in thus deducing that coated flasks cannot be reused after trypsinization? Are any of the alternative detachment reagents an exception to this?

Interesting question. Since I don't have a real answer at the moment, I would say it depends strongly on the incubation time. The longer you digest, the more of the coating will be digested, too.

@Chris Good point, edited.

Generally the coating is of poly D-Lysine. Proteases act only on L-amino acids. Moreover the amide bond in PDL is between the ε-amino group & carboxyl instead of the α-amino group as in peptide bonds. So, I guess nothing should happen to the usual coated flasks. I have used the same flask for 2 rounds of trypsinization, and the cells seemed to be fine.

A small correction: PDL is not ε-amide, nonetheless the D-conformation would make it resistant to protease.

@WYSIWYG That's an interesting point. However, what about the coat I mention? Corning fibronectin is isolated from human plasma, Corning collagen I is from cow plasma, and NEB does not clearly explain where they get their albumin (they say "fraction V") but I think it's also purified from an animal product. I thought all of these would come out as L-isomers.

Generally the coating is of poly D-Lysine. Proteases act only on L-amino acids. So, I guess nothing should happen to the usual coated flasks. I have reused the flask even after 2 rounds of trypsinization, and the cells seemed to be fine.
In your case, the matrix is made of proteins isolated from animal sources. They are susceptible to proteolysis. You are right to assume that these flasks should not be reused. If you have a shortage of flasks then you can buy uncoated petriplates (which are cheaper) and coat them yourself.

You should check the composition of the coating by using trypsin, e.g. poly-L-lysine or poly-D-lysine are usually applied:

Polymers of both D- and L-lysine are used to coat solid surfaces.
  Poly-L-lysine has been reported to improve the protein coating of
  ELISA plates. 6,7 However, in culture applications, certain cells can
  digest poly-L-lysine. In this situation, poly-D-lysine should be used
  as the attachment factor so that the cells are not disrupted by
  excessive uptake of L - lysine. The lower molecular weight
  poly-D-lysine (30,000 - 70,000) is easier to use because it is less
  viscous in solution, but the higher molecular weight poly-lysine
  (>300,000) provides more attachment sites per molecul e. The molecular
  weight poly-D-lysine often preferred by users is the 70,000 - 150,000.

Poly-D-lysine Hydrobromide - Sigma

Trypsin does not seem like to hydrolise poly-D-lysine. Roughly it is specific to L-Lys and L-Arg, so if your coating contains these amino acids (in your case it does), than it will be degraded.

Trypsin (EC3.4.21.4) is part of the serine protease family. Trypsin
  cleaves lysine and arginine at the C-terminal side of the peptide. The
  hydrolysis rate is slower if an acidic residue is on either sides of
  the cleavage site and no cleavage occurs if a proline residue is on
  the carboxyl side of the cleavage site. Trypsin optimum pH is pH-7 to
  9. Trypsin will also hydrolyze ester and amide linkages of synthetic derivatives of amino acids such as: benzoyl L-arginine ethyl ester
  (BAEE), p-toluenesulfonyl- L-arginine methyl ester (TAME),
  tosyl-L-arginine methyl ester, N-α-benzoyl-L-arginine p-nitroanilide
  (BAPNA), L-lysyl-p-nitroanilide, and benzoyl-L-tyrosine ethyl ester
  (BTEE). Serine protease inhibitors that inhibit recombinant trypsin
  include TLCK (N-p-tosyl-L-lysine chloromethyl ketone), PMSF
  (phenylmethanesulfonyl fluoride), benzamidine, soybean trypsin
  inhibitor, and ovomucoid.

Trypsin Human, Yeast - ProSpec, or Sigma here

After incubation with 1mg/mL trypsin solution at 37°C for 1h, neither
  PLL nor PDL was found to be hydrolyzed, as indicated by the constant
  number of molecules found on the surface. The reason is that the
  entire polylysine chain was adsorbed to the surface, and steric
  hindrance and electrostatic repulsion prevented trypsin molecules from
  approaching the cleavange sites. To make polylysine exposed and
  available to trypsin digestion, a DSU SAM surface was created. A
  uniform coating of 5nm chromium and 30nm gold was first introduced on
  the slides. On top of that metal coating, an amine-active
  cross-linker, DSU SAM, was formed to covalently immobilize
  AF532-PLL/PDL molecules. After the free peptide molecules were
  removed, the slide was incubated with 1mg/mL trypsin at 37°C for 1h.
  The trypsin and cut polylysine fragments were then thorougly washed
  off. Intact PLL and PDL molecules had similar fluorescence intensities
  and surface number densities before trypsin was introduced. However,
  it is clear that trypsin digested PLL but not PDL. From over 30 images
  of different areas of the slides, for PLL the average numbers of
  molecules counted were 227±16 and 0 per frame before and after
  hydrolysis, respectively. In contrast, the corresponding numbers for
  PDL were 241±15 and 234±20 per frame, respectively. As explained in
  Emil Fisher's analogy of the lock and key, the L-isomer can fit the
  active site of trypsin bettern than the D-isomer. One reason is that
  only the L-isomer undergoes a coil to α-helix transition upon binding
  with the enzyme, while the D-isomer remains disordered.

2008 - Applications of single-molecule detection in early disease diagnosis and enzymatic reaction study

So the result depends on the type of the coating. Btw. I think the easiest way to decide would be to check it with an experiment. (Note that I know nothing about coatings, just trypsin.)

In case someone finds this thread and wants an answer. In this paper (J Biomed Mater Res A. 2005 Oct 1;75(1):1-13.) the authors show that trypsinization does indeed remove the protein coating from the culture vessel.


text:
What's up with all the vague protocols?
I have lost count of how many protocols I've seen, including those supposed to be professionally written (such as manuals that come with kits from well known brands, or methods sections of papers in respected journals), that outright fail to give unambiguous instructions. Some common examples are:

Give centrifuge speed in RPM instead of RCF, and not say what rotor or centrifuge it is.
Say to spin a sample at "maximum speed".
Use subjective time periods, e.g. "incubate briefly" (is one minute brief enough or does it have to be five seconds?)
Subjective quantities, such as "get a good amount of cells" (!!!)
Give time ranges without explaining the consequences of the choice, such as "5-10 minutes" (is it 5 or 10? which one???).
Say "mix well", without specifying if vortexing is okay.
Say "mix well, don't vortex", and don't explain what mixing technique I'm supposed to use.
Give urgent-sounding warnings, such as "don't touch the pellet!", without explaining what happens if I do it or how to fix it (do I need to start over? will I just get 5% lower yield?).
Give urgent-sounding warning, without explaining how to actually heed the warning ("dry the pellet, but do not over-dry it!")

It is in fact extremely rare that I ever see a protocol that has none of these issues. It almost never happens.
It is extremely important that scientific results be reproducible, and it seems like you are opening yourself up to a lot of trouble with an ambiguous protocol. What if somebody fails to reproduce your results, not because your experiment wasn't legitimate, but simply because you left out some crucial detail from the protocol you gave them? You would look bad, and for no good reason.
So why is it so common for protocols to be ambiguous? Is there some nuance to this that escapes me, or do people just not care? How do you follow a protocol that left out crucial information so as to be impossible to follow? Or are you supposed to have amassed a sufficiently vast reservoir of practical knowledge that you can draw on it to "fill in the blanks" on the fly?

As a counter argument to the hold: I am specifically interested in the personal experiences of researcher who have encountered this problem far more often than I have (perhaps I have failed to communicate this adequately). I am hoping that these anecdotes will be useful to me, and other novice experimentalists like me. As such, I think it can qualify (perhaps with some revisions) as a good subjective question.

I agree. This is more a meta question for biology research, so I don't think it's completely off-topic.

@Karolas Incidentally, the "boring lab questions" have always been a bit of an unclear case as to whether they fit. I believe a Meta discussion concluded that it's best to include them here, as opposed to say Academia@SE or a separate SE site. That said, the hold appears to be not for topicality, but subjectivity (and to be honest I don't understand how it's opinion based, but that's another matter).

This is too long for a comment, so I post my thoughts about this here:
This falls into different important parts here: One is an insufficient understanding of the techniques on which the method is based. This makes it hard to decide which steps are important and which are not. One prominent example would be the use of EDTA in DNA gel running buffers. This recipe originated from RNA research (where you need the EDTA) which where then simply used for DNA as well. Since it worked somehow, it was never really changed.I have seen enough people in the lab clinging to old photocopies of protocols without knowing why they do certain steps.
And the other (connected) issue is that protocols are usually passed down through labs. Things are then done in a certain way because they have always done in this way (with some changes in the protocol probably not even documented) and are not changed. People are even told to use the exact routine, even if this makes absolutely no sense.
In publications there may also be another thing which comes into play: The fear that someone uses the own methods and will then be faster than the own group. At least some groups only publish incomplete and vague methods because of this reason. Then it's a thing of space: There are character limitations in publications and when you need to save a few hundred characters when the article is too long, it's much easier to shave the methods than the discussion.

Thanks, this a quite informative comment/answer. The EDTA example is a very good one that I had noticed myself. I'll wait for other answers, since the question is probably more useful as "What do you do if a protocol is vague?" rather than "What is the reason for protocols being vague?".

@Superbest As I said, it's more like a comment, but too long for it.


text:
Why do humans enjoy spices?
It seems that many flavor and food preferences can be explained in the context of regulating feeding behavior. Generally, organisms tend to enjoy those foods which are optimal for them to feed on and provide the best nutrition. There are well-known exceptions to this, such as:

Artificial chemicals (eg. the supposedly sweet-tasting but deadly polyethylene glycol) which are very rare in nature, thus there was no opportunity for an appropriate taste perception to evolve
Nutrients which are desirable in moderation but dangerous in excess (eg. sugar), but have only become readily available recently thanks to technology (thus once again moderated consumption has not had opportunity to evolve)

But humans in particular also seem to enjoy consuming a large variety of foods that one would expect to be unpalatable or mildly harmful. For instance various peppers, spices, hot sauces, wasabi, mustard and so forth, don't appear to provide much of a nutritional benefit. Indeed their chief property of interest, the spicy flavor, is a defense mechanism: The plant attempts to make itself unpalatable or toxic to deter predation. Why is it then that this very defense mechanism has ironically become prized as a food ingredient by humans, to such an extent that wars have been fought over access to spices? And why is it that humans do not consider (for instance) pure, fresh, raw meat to be more delicious than meat with seasoning or condiments?

There has been a similar question (see comments) on here but that has also not attracted a good answer. I think this exemplifies the enduring interest in the subject and as such I'd like to keep this question open to stimulate a better response from more recent visitors.

I don't know enough of this, so I won't answer. However, I know that one hypothesis is pathogen avoidance. I don't know how much truth there is to it, but it is sometimes claimed that spices help against pathogens. Proponents of the antimicrobial hypothesis (as it is called) point for example to the fact that spicy food is more common in warmer climates as evidence for the hypothesis (the point, of course, is that pathogens are more common in warmer climates). However, I don't know whether there is something to the hypothesis or not.

@John Incidentally, also unanswered.

actually there are two answers


text:
Is a naive immune system equally able to handle new antigens as an educated one?
This is a variation of the "does the immune system run out of memory" question.
Here's a (possibly imperfect) thought experiment: You take two twins. One of them lives in a bubble from birth. One of them is Mike Rowe from Dirty Jobs, and gets exposed to all sorts of antigens as well as vaccines. When they are 30 years old, you expose both of them to an antigen that neither has seen before. What happens?
PS: Note that while this example is illustrative, my question is really about whether there is any way at all in which the response of a naive immune system to a novel antigen is different from that of a very educated immune system (which has also not seen the antigen before). For instance, would the same amount of antigen be required to stimulate the immune system? Would the antibody count several months or years post-exposure differ?

Of course, we've never done this experiment (bubble boy without an immune deficiency), but I'd speculate that the regulatory environment for the immune response would be quite different. It's hard to say whether the 30 year old immune virgin would react to exposure like an infant, or something different entirely, but you can't just consider the novel antigen and the immune cell that recognizes it. In vitro, in standardized conditions, you would expect a naive B or T cell from either brother to react to a novel antigen in the same way, but that's not what you're asking.

They will both go through a primary and secondary immune response. So first low affinity antibodies will bind, the corresponding b cells will undergo affinity maturation, somatic hypermutation until high affinity (perfectly fitting) antibodies are available and these antibodies will finally undergo class switching.
Depending on the antigen an innate immune response will also be triggered as part of the first line of defense. There is no difference in the immune response between these two hypothetical brothers.

While the initial response would be the same because neither person has corresponding antibodies, would there be a difference in the amount of time that it takes the killer T cells to respond and destroy the antigen? Bubble boy never uses his killer T cells and Mike Rowe would use them all the time. Would that make a difference in response time or the quantity of killer T cells?

Not when we assume that both have never seen this antigen.

I think this is the right answer, barring cross-reactivity. In other words, Brother Ed (educated) may have not have seen a specific new antigen, but he may have been educated with another antigen such that his antibodies cross-react with the new one.  So, on balance, I'd err on the side that Ed might indeed react.  Feel free to add if it helps.

This answer neglects the general changes that occur in immune cell and antibody populations resulting from 30 years of exposure to the environment. Cross reactivity is one issue. There are many others, e.g., the regulatory effect of the entire population of the gamma fraction of plasma, and changing populations of $T_{reg}$ and Th17 cells. The adult immune system is quite different from an infant's immune system, and much of this appears to be related to cumulative exposure to non-self antigens. It's not as simple as whether or not you've been exposed to a specific antigen.


text:
Why don't fish groom each other?
Fish are often plagued by external parasites, which are presumably difficult for them to remove.
There are well known cases where large fish come to coral reefs and allow smaller fish to pick off their parasites. See below a moray eel being "cleaned" by a shrimp.

Some fish, like sunfish, even get cleaned up by birds: https://www.youtube.com/watch?v=U60obmWODLQ
But on land, we have many social animals that solve this problem more directly by grooming each other. How come the fish never seem to do this? Many of them are already social, and I imagine they wouldn't have much trouble digesting the external parasites. Why don't they groom each other?

They probably think that's gross.

All cases of same species grooming I know of involve animals with a certain amount of dexterity. For example (images from wikipedia):

Macaw beaks:

Primate fingers:

Even ponies rubbing each other:

In all of these cases, the animals involved have the right tools for the job. fingers, beaks and prehensile lips can all close in on a parasite and remove it with precision. how exactly would you expect a shark to do this (image from the guardian)?

Sharks can and do rub themselves against rocks to get rid of dead skin but they simply don't have the tools for the kind of detail work that the smaller fish can do for them. The same applies to other fish. I think you will find that at least in most cases, fish that use client species to groom themselves wouldn't be physically able to do the same job themselves. It's all a matter of the right size and the right tools.

Note that this is pure speculation, I have no references to back this up, it just seems reasonable. I would not be surprised if some fish did actually indulge in social grooming, it's just harder for the reasons outlined above.

A good answer, but keep in mind that the question was about fishes in general. I assume that the OP is talking about the more subordinate species of fish.

@VatsalManot yes, but I think it's applicable to all. In order to be able to eat parasites, you need to be small enough to get at them. Presumably, if you're the same species, you will be too big. Still, as I said, this is pure speculation.

As you correctly noted in your answer, symbiosis is a viable solution for the size to size ratio problem.

Perhaps it has something to do with fish slime coats.
Fish are covered in a thin layer of mucus which helps with immune system function, etc. According to these guys at least, who admittedly are not exactly a scientific authority.
Perhaps grooming as a social behavior would disturb the slime coat more often than it would help remove parasites? Or it's dangerous for other reasons? (Some fish are very territorial)
Some(most?) fish are just incapable of grooming other fish of the same size and shape. I mean look at this guy. The moray eel above has a jaw much larger than that of the entire shrimp that is grooming it, so perhaps picking parasites off things with such a jaw is like cutting your fingernails with a meat cleaver?

But the fish still get groomed, by other species. Are you saying that they would loose the layer if a fish did the grooming but not when done by a shrimp or seagull?

You know the more I think about it the more I suspect mouthparts are to blame. A marlin for instance can't groom anything, much less another marlin. They just don't have the right teeth/jaw for it.

Yeah... but then at some point there was a bifurcation, they could have chosen a suitable mouth for grooming or a mouth for other stuff to do. Maybe the severity of having parasites, which I don't know, versus other dangers has something to say in this.

I mean grooming parasites off of other members of your own species can't be a viable food source for your whole species. Specialist mouthparts for eating any other food would be better, so I imagine it's just a thing that might be nice to have, evolutionarily speaking, but ultimately shrimp are "good enough" at it.

Something from my imagination: Probably the first fishes were of small size with some of them evolving to be big. The variation in the sizes of the fishes is larger compared to the variation in the sizes of mammals(picture elephants and rats with whales and tiny fish). That being said, if you'd have bank of small fish staying in one place and all grooming each other, a bigger fish would swallow them with one bit(as whales eat). This does not happen on land with, say monkeys, because it would be too big of a load for  a tiger or an eagle to snatch both of them with one move. In conclusion, the ways of predators in oceans(trickier ambush tactics, faster speed attacks) and variations in sizes might have made this more of a disadvantage than an advantage underwater compared to on land.

Regarding predators: Many fish such as herrings already live in large, dense groups - and they do get swallowed wholesale by whales. This apparently is not enough to deter the schooling behavior, though.

But herrings constantly move, they would have to be able to move and groom at the same time.