What hair color will result in someone inheriting both blond and ginger genes? Both the genes for blond hair and ginger hair are recessive, so they need both parents to give the same gene for it to take affect. What happens when a person has 1 copy of a recessive gene and another copy of a different recessive gene.

They don't have enough of the recessive genes to have either blond or ginger hair, but they don't have a dominant gene to "take charge"?

Hair color is not so simple as that.  Most traits, especially those as complex as color, are controlled by many alleles at many loci.  That's why there are different kinds of brown, blond, and red hair in the population.  There is no "hair color gene."  A fascinating paper came out a few years ago, identifying dozens of SNPs playing a role in hair and eye color.  It's a deep, deep rabbit hole that we have only begun to plunge into.

EDIT: To summarize, it's very complex.  This paper performed genome-wide association scans looking at two comparisons each for eyes (Blue and green, blue and brown), hair (red or not, blond or brown), and skin (freckles, sun-sensitivity).  The researchers looked in a group of Icelandic and Dutch individuals, which means they only looked at a small portion of human variability (i.e., very few African or Asian genomes, for example).  Still, just from those simple comparisons, their scans:

  revealed 104 associations that reached genome-wide significance, accounted for by 60 distinct SNPs, of which 32 showed genome-wide association with only one pigmentation trait, 12 with two traits and 16 with three traits.

That is to say, they found 60 DNA bases that explained their data.  Roughly half of those only affected one thing (eye, or hair, or skin, but only one), a fifth of those single base changes contributed to two different traits, and a full 25% of those SNPs were related with three traits.

That's still pretty hefty.  Basically, they found 60 things that can affect hair, eye, or skin color, and some of those can affect some or all of those at the same time.  And they only looked at people from two countries.  Here's a figure where they summarize the seven strongest SNPs; you can see how tricky it can be to explain colors.


why do we tighten out muscles against cold? When I'm in shower and I want to open the cold water on myself suddenly I make my muscles so tight before I open the water and that helps so much in being able to handle the shock. Why does tightening of muscles help in handling the shock.

Consider most animals instinctively recoil from unpleasant sensations. Resisting this often involves tightening the muscles. Think about the last time you had to get a shot or pull a splinter out of the skin, you often tighten the muscles in an attempt to resist your own instinctual reaction. Even non-physical reactions like resisting fear or disgust often have similar responses, the mind and body do affect each other. Physical actions can effect mental states. Tensing muscles has been shown to have a direct effect on our willpower.


Databases for metabolic pathways of human disease Which databases contain the metabolic pathway of human diseases?
I have searched Metacyc and KEGG but didn't find the appropriate metabolic pathway.

NCBI BioSystems help file contains a list of their sources:

http://www.ncbi.nlm.nih.gov/Structure/biosystems/docs/biosystems_help.html#SourceDatabases

Please specify what you need as stated in the comments as it is almost impossible to give you more (relevant) information then this.


How does a cell create/gain its initial ribosomes for protein synthesis? I did some quick google searches for how a cellular organism generates or acquires its first ribosomes, but I found nothing. For instance, do the organisms initiating replication form extra Ribosomes to pass on to the created organism?

From the comment section:

Cells divide and when they do the two daughter cells will not only have copies of the DNA but also of the organelles, the cellular machineries and the cell membrane which implies that yes the daughter cells receive also ribosomes. The replication happens during the interphase.


Why are hard boiled eggs so homogeneous? A eukaryotic animal cell is a complicated piece of biological machinery.  Some major structures inside of the cell (see the image below) include: the nucleus, mitochondria, Golgi vesicles, and various tubular structures.  Why then is the single-celled, unfertilized chicken egg so homogeneous when it is cooked (or before)?  The only major structure I can recognize is the cell nucleus.

*Image Credit: "Animal cell structure en" by LadyofHats (Mariana Ruiz) - Own work using Adobe Illustrator. Image renamed from Image:Animal cell structure.svg. Licensed under Public domain via Wikimedia Commons - http://commons.wikimedia.org/wiki/File:Animal_cell_structure_en.svg#mediaviewer/File:Animal_cell_structure_en.svg

Disclaimer: This is my understanding of the egg anatomy as a general biologist. There is most certainly better references and sources out there to explain this (please add better references if you know of any).

If I understand you correctly, your question is why we do not see cell organelles in a cracked or boiled egg. If so, your question seems to stem from a misunderstanding of what the egg white and egg yolk represents. A chicken egg is not simply an enlarged cell, and the egg yolk is not the cell nucleus.

When an oocyte matures in the chicken ovary, it stores yolk inside the cell and therefore enlarges. The yolk is therefore part of the oocyte cytoplasm. However, as it enlarges, the yolk is separated from the germinal disc, which holds all the other cell organelles (including the nucleus). The germinal disc is seen as a small white area on the egg yolk. Eventually, when the oocyte has accumulated enought yolk, it disattaches from the ovary (ovulation) and goes into the hens oviduct. This process is happening continuously, and oocytes of different stages of maturation are present on the ovary, which can be seen in this image:

(image from Chickscope: Formation of the Egg. University of Illinios)

When the oocyte passes through the oviduct it builds up layers of egg white (albumen) and other supporting structures. The shell is formed last in the shell gland, which is located at the end of the oviduct. Therefore, the egg white and the shell is formed externally of the oocyte and the egg yolk.

So the reason why we do not see more structures in a boiled egg is that the majority of the egg is yolk and egg white, which are both structures to store energy ment for a growing embryo (mainly protein and fat). It should also be noted that oocytes in most (all?) animals contain yolk granules, but the storage of yolk is most extreme in birds (see this webpage on animal development from State university of New York for a short comparison).

It should also be noted that an egg that is fertilized will naturally contain more than one cell, since the embryo will have started growing.

References:

Chickscope: Formation of the Egg. University of Illinios (webpage)
Chickscope: The yolk. University of Illinios (webpage)
Chapter "Eggs" in Johnson et al. 2002. Molecular Biology of the Cell. 4th ed. Garland Science, New York
Wikipedia: Egg
Animal development. State university of New York (webpage)


Where and how is information about pathogen immunity stored in a cell? If all of the DNA is being used, then how would the cell be able to store new information about pathogens in DNA? It's like a full hard drive that can't hold any more. So does the cell just compress the information about the pathogens and then just adjust the existing information about pathogens?

All the body does is produce a ton of cells that can recognize single antigens. Each time you encounter pathogens, some of these naïve cells contact antigen that can activate them. The activated clone replicates itself, forming effector cells that can deal with pathogens.

As the infection is cleared and the population of effector cells begins to contract (i.e. many die off or become anergic), some of them undergo changes which alter their migratory pattern and longevity. Some can stay in the tissue that was originally infected as tissue-resident memory cells. Some home back to the lymph node and hang there as central memory cells. The lineage is affected largely by chemical signals being produced by the tissue and other immune cells in the vicinity.

Upon re-encounter of the same pathogen, if it has some of the same antigenic determinants as the original infection, these memory cells are already known to be specific to them. Encountering the same antigen will cause these memory cells to undergo another round of clonal expansion, producing more effector cells and additional memory cells so the process can repeat. These events can be limited by telomere length or inhibitory molecules, as a caveat.

The key understanding is that the immunologic memory is actually stored in the repertoire of long-lived memory cells, and in part results from recombination events at the T or B-cell receptor locus during their maturation before they're released as naïve cells.

See: Abbas (2014). Cellular and Molecular Immunology, 8th ED., many different chapters.


What factors may lead to a difference in whole-cell potency compared to cell-free potency? For studies of protein-ligand binding, the reported whole-cell potency may be higher or lower compared to measured cell-free potencies.

For decreased potency, this may represent an increase in non-specific binding of the ligand. Are there other factors that may contribute?

On increased potency, I've noticed this applied to the BACE1 protein in which the IC50 may go on the micromolar scale in a cell-free assay to nanomolar scale in a whole-cell assay. This seems counterintuitive to me. Are there possible reasons for this trend?

You are correct in saying that whole-cell potency and in vitro/cell-free potency often differ by quite a bit. There are actually a lot of factors that can contribute to this, but I'll try to give a couple illustrative examples, for increased and decreased potency (when moving from cell-free to a whole-cell assay).

When moving from cell-free to whole cell assays, decreased potency is the more common outcome. As you mention, a big reason is just that you get a lot more things the drug can bind to, so you tend to have less drug effectively engaging the target. However, there are other factors at play as well. Ultimately, the main reason that one sees decreased potency in the whole-cell format is that one is often asking for something fundamentally different than what was asked for in the cell-free assay.

For example, let's say you do some CRISPR of RNAi screen in cancer cells, and you find that if you shut down gene X, the cells die. You look it up, and gene X codes for an enzyme.

So you think, "Great! I'll design an inhibitor for the enzyme, and then kill the cancer cells with that!"

In order to screen for inhibitors and test their effect on this enzyme, you set up an in vitro with purified enzyme, substrate, and some way of measuring the generation of product. You screen, find compounds, and optimize your lead. You eventually end up with a compound that has an IC50 of 1 nM in this assay. Then you decide it is time to move into cells. You treat the cancer cells with the compound, and you notice that your IC50 for cell death is 100 nM - 100x what it was in the original assay. The reason is that you are asking much more of your compound.

In the first assay, the compound had to bind to the enzyme, which may have been the only protein in solution, and inhibit it. You were directly measuring enzyme activity. In the second assay, the compound had to diffuse through the cell membrane or find some other means of getting into the cytosol, where the target protein resides. Then, despite the complex milieu in the cell, it had to bind that specific protein and inhibit it. But inhibiting the protein isn't enough. It has to inhibit the protein enough to kill the cell. Maybe the cells die when the enzyme activity is 50%, in which case you would expect your IC50 values to be fairly close between assays. But maybe it doesn't. You may need 70 or 80% inhibition before the cells start to actually die. Plus, the cells may not go down without a fight. Maybe they up-regulate expression of drug-efflux pumps, which are ATP-powered proteins that literally pump small molecules out of the cell. This reduces the effective concentration of drug you are giving the cells. There are also many other adaptations that the cells may undergo to improve survival, which are beyond the scope of this answer. So what you are demanding from your compound in the whole-cell assay may actually be much more than in the cell-free system.

The other effect - seeing increased potency in whole-cell vs cell-free conditions is much less common. Without seeing the exact study you are referring to, it is difficult to comment. However, one thing to remember about BACE1 is that it is part of a huge complex that is embedded in the cell membrane. Reconstituting this complex in vitro is non-trivial, and it may be that the complex is not functioning the same as in the cell depending on how the reconstitution was performed. For example, maybe BACE1 binds better to the drug only when a binding partner is present that stabilizes a conformation suitable for inhibitor binding. It could also be that the inhibitor is actually targeting another protein in the complex that is not present in the cell-free system.

Anyway, I apologize if this was a bit long, but I hope this answered your question and shed a bit of light on the complexities of assay development and drug development.


Did the Swedish cod fishery expand in the past years? The Marine Stewardship Council states that the cod fishery in the Eastern Baltic sea recovered well and issued it's MSC certificate to the Swedish cod fishery in 2011 for that region. (MSC 2011)

Data downloaded from EUROSTAT shows that Portugal, a main importer of codfish and -products, imported less and less from Norway (besides Iceland and UK the main supplier) (FAO 2006); dropping from around 20,000 tons (2001) to < 1,000 tons (2011) and more and more from Sweden; < 5,000 tons until 2003 versus > 30,000 in 2010 and 2011.

This trade data does not necessarily show the origin of a product but rather the country that is selling the fish. I wonder if either the Swedish cod fishery expanded in the past few (~ five) years; Portugal changed it's main supplier from Norway to Sweden for whatever reason; or Sweden buys cod from Norway and distributes it.

Depending on this the answer may not be so closely related to biology but I hope to get an idea here.

If by 'fishery' you mean "amount of fish caught", the answer is a qualified no. Sweden's catch has been stable or perhaps slightly increasing since a low in 2005, but the catch is still much lower than a decade ago (Statistics Sweden). This is presumably due in large part to the quotas set on Total Allowable Catch for various sea regions.

If by 'fishery' you mean "amount of fish in the sea", the answer is a qualified yes. Most Swedish cod catch (>90%) comes from the Baltic, where stocks have been recovering since 2006 after steep declines in the eighties (ICES full report and executive summary for Eastern Baltic). Presumably, this recovery is also due in large part to the quotas set on Total Allowable Catch, i.e. to the reduction in cod mortality due to fishing.

Sweden's cod catch for all regions, and the ICES estimated Spawning Stock Biomass of cod in the Eastern Baltic. Both are in thousands of metric tons, but note that the scales differ by a factor of ten)

No idea how this is affecting import/export, although Statistics Sweden might have that data. One biology related possibility is that Eastern Baltic stocks (presumably accessed more by Sweden) are doing better than North Sea stocks (presumably accessed more by Norway), but that's just a guess, you'd have to check the data.


Identify plant stem parts What are the names of the parts A, B, C and D?

This is not homework. I am not a biology specialist. Looked through books for than 30 min. Most of them are schematic diagrams, not photos. Furthermore, the vascular bundle is normally shaped like a cone but this one is crescent shaped.

I reckon that picture as cauloma. Because it has a trichoms on epidermis. A_ corical parenchyma B_Phloem C_ xylem D_pitch. I hope it will help you.


How often do retrotransposons jump in human cells? If I followed the life of a typical cell in my body, how many retrotransposon jumps would I observe per day? I'm only interested in a rough order-of-magnitude estimate: should I think of it as a common event that happens basically all the time in most of my cells, or is it a rare event that happens only occasionally in my body?

For just rough order-of-magnitude, try this reference. Their experimental design seems to maximize transpositions so it should be a reasonable upper bound.

There is a lot of variability, but some retrotransposons jumped in ~1000 cells per million, others only a few per million such that they were difficult to detect, after about 1 month in HeLa cells.

The same reference gives an estimate of 10,000 retrotransposon elements in a mammalian genome, though, again, their transposition frequencies vary considerably.


What are housekeeping and constitutive genes? I have come across two set of definitions which are not contradictory but different.

From wikipedia:

  A constitutive gene is a gene that is transcribed continually as opposed to a facultative gene, which is only transcribed when needed.

  A housekeeping gene is typically a constitutive gene that is transcribed at a relatively constant level. The housekeeping gene's products are typically needed for maintenance of the cell. It is generally assumed that their expression is unaffected by experimental conditions. Examples include actin, GAPDH and ubiquitin.

My question from these definitions: What does 'transcribed at a relatively constant level' mean? Does it mean that a constant level of gene product is maintained in a cell? I can't understand there meanings atal.

Again,according to Oxford dictionaries

  Constitutive Genes are genes that are expressed following interaction between a promoter and RNA polymerase without additional regulation.
  (Oxford Dictionary of Biochemistry and Molecular Biology)

  Housekeeping genes - Constitutive loci that are theoretically expressed in all cells in order to provide the maintenance activities required by all cells: e.g., genes coding for enzymes of glycolysis and the  and the citric acid cycle.(Dictionary of Genetics)

These definitions do not tell whether they are continually transcribed or the synthesised products are present in constant amount.

Which one best define them?

I think the best answer is both: they are continually transcribed at a rate that maintains the synthesized products at a (roughly) constant level. These terms are really just descriptive terms, there is no true biological dichotomy, it's just that some genes are expressed pretty much all the time and others are only produced when needed, for example genes for proteins needed at a particular stage of the cell cycle.

As @canadianer mentions in a comment, there are also other forms of post-transcriptional regulation, such that constitutive transcription doesn't necessarily mean constant production of protein at an equal rate.

Wikipedia has quite a list of different "housekeeping genes" and you will see the list is quite extensive. It certainly isn't true that all of these genes are expressed at exactly the same levels all the time, it is simply that their expression is consistent enough to be used as an approximate standard when comparing expression levels.

If I could produce a definition that reflects reality better than the ones you found, I would amend the Oxford definition to something like:

  Constitutive Genes are genes that are expressed following interaction between a promoter and RNA polymerase at a level that doesn't seem to vary much across cells of the same type, doesn't require a very special transcription factor, and so far biologists haven't found an experimental condition that greatly impacts the expression level.


By what mechanism does elevated homocysteine level accelerate thrombin formation? It has been stated that elevated homocysteine level accelerates thrombin formation. By what mechanism does this happen?

According to a heavily-cited paper (below), homocysteine reduces the expression of thrombomodulin on the surface of endothelial cells.

Thrombomodulin binds to thrombin, and the resulting complex does not promote coagulation, but instead activates protein C. Protein C has an anticoagulant effect. Thus reduced levels of thrombomodulin will result in increased levels of free thrombin (promoting coagulation) and in reduced levels of protein C (also promoting coagulation).

I haven't found any evidence that homocysteine has an effect upon thrombin formation directly.

  Lentz,SR and Sadler, JE (1991)Inhibition of thrombomodulin surface expression and protein-c activation by the thrombogenic agent homocysteine. J. Clin. Invest. 88:1906-1914

  Abstract Elevated levels of plasma homocysteine are associated with both venous and arterial thrombosis. Homocysteine inhibits the function of thrombomodulin, an anticoagulant glycoprotein on the endothelial surface that serves as a cofactor for the activation of protein C by thrombin. The effects of homocysteine on thrombomodulin expression and protein C activation were investigated in cultured human umbilical vein endothelial cells and CV-1(18A) cells that express recombinant human thrombomodulin. Addition of 5 mM homocysteine to endothelial cells produced slight increases in thrombomodulin mRNA and thrombomodulin synthesis without affecting cell viability. In both cell types, thrombomodulin synthesized in the presence of homocysteine remained sensitive to digestion with endoglycosidase H and failed to appear on the cell surface, suggesting impaired transit along the secretory pathway. In a cell-free protein C activation assay, homocysteine irreversibly inactivated both thrombomodulin and protein C in a process that required free thiol groups and was inhibited by the oxidizing agents diamide or N-ethylmaleimide. By inhibiting both thrombomodulin surface expression and protein C activation, homocysteine may contribute to the development of thrombosis in patients with cystathionine beta-synthase deficiency.


Is there anyone discovered new drugs by actively create mutations in drug-producing organism? Recently I was reading about drug discovery.

As far as I know, there are currently 2 sources of creating new compounds by:

Screening from natural sources.
Synthesizing by add/remove/replace-ing the functional groups of a known compound using chemical processes.

On the other hand, molecular pharming is the process of producing drugs by integrating the drug-encoding genes into bacterial (typically E. coli) genome.

I came up with the idea that if we create mutations in these drug-producing colonies, by UV light for example, eventually by chance we can obtain some new compounds once the mutations occur in the drug-encoding region or related genes.

I want to search in the previous studies for those who has come up with this idea already, I tried with several keywords and there's no luck.

I would want to ask is this idea practically possible? How high is the chance of having new compounds compare to screening natural sources and chemical systhesis? And if someone has already done this study, can you please provide me some references on this matter?

I'd say this is possible, but not really practical. Mutating genes by UV light is not that hard, it's just the screening for the (new) compounds that makes it difficult. You would probably be better of creating diversity using established chemical methods.

Usually UV mutagenesis is done for whole organisms, but some people probably also tried this for single genes (even though they'd hit the whole genome). This is the easy part; you could get an enormous amount of diversity with very little work. Even though mutations that change enzymatic products are probably much more rare than mutations that change substrate specificity or product chirality, people find those mutations (example from the top of my head: p450 hydroxylation patterns, although they probably used targeted mutagenesis).

Determining if a specific compound is produced by an organism is also not very hard. You break all the cells, put the solution on a column and check with your favorite analytical method whether or not your compound is in there. Checking for new compounds is much harder. You need better analytical methods such as MS/MS as you don't have analytical standards, and the adapted molecule might not even be detectable with the analytical method you used for the starting molecule. We are very good at detecting needles in haystacks, but determining if there is a needle, a stick, or maybe a piece of hay from another species in the haystack is much harder. You'd already have to predict what kind of altered molecules you expect to find.

When you have successfully done all this, you have identified a single new molecule. Nowadays, people use libraries with >100,000 compounds to screen against their disease protein of interest.

The idea of mutating enzymes to produce new products is not that strange, people work on this, publish, find a lot of interesting things and we learn a lot about enzymes. As an approach for drug discovery this approach is just not high-throughput enough.


Tc and Th1 interaction and viral immune response Tc is T cell which can give T killer cells and T helper cells.
T helper cells (Th1) see the pathogen presented by antigen presenting cells (dendritic cells and macrophages).
They then secrete antigens to kill the pathogen.
If there is memory from previous interaction, then it will be easier to protect.
However, since some viruses replicate fast (RNA particularly), this memory benefit is often lost, like in the case of influenza virus A and B types.
However, I am uncertain how to explain this immunology with viruses.

How can you explain this general viral interaction better in the immune response?

I have these pictures in mind:

and

PlaysDice's answer:

Antigen presenting cells migrate from skin/mucosa to secondary lymphoid organs like lymph nodes/spleen/GALT and drive T cell activation and maturation.
T helper cells with CD8 and MHCII complex recognise the virus and kill it.

I think this is what is happening, for instance in HIV infection:

where

dendritic cell (ADCC) presentation of HIV infected CD4+ to MHCII and T helper cell
T helper cell activates cytokine release
Natural killer cells come and lyse the HIV infected CD4+ T lymphocyte


Congenital blindness due to retinitis pigmentosa - does it exist? Retinitis pigmentosa (RP) patients typically become blind after a period of years in which their eye sight slowly deteriorates due to photoreceptor degeneration. Generally RP patients develop night-blindness first, then tunnel vision, after which finally the central eye sight diminishes leaving them with basically no eye sight, barred some crude residual light perception. The wiki page on RP has more information when needed. Typically, the process from diagnosis of RP to (near) complete loss of eye sight takes years to decades.

However, Chebat et al. (2007) make mention that their study group, consisting of congenitally blind subjects, includes one person with RP (see table 1 in the linked article). Hence, this implicates that this particular subject was blind from birth due to effects of RP.

Is anyone familiar with newborns blinded by the effects of RP?

Reference
Chebat et al. Neuroreport 2007;18:1901-4

I have only ever heard of one case where RP caused blindness in a newborn. Unfortunately, I am unable to release the name or any details of the patient because of privacy issues and so forth.

Usually blindness from RP comes after a few years of life (as you said), making blindness from birth (or even early infancy) very rare.

I can tell you, however, that the formerly stated patient suffered from type I Usher Syndrome, if I remember correctly. I apologize for my inability to provide you with more specific details on this.

I don't know how much this will help in your search, but I sincerely hope that it does.

CDB


Definition of a Katal (unit of enzyme activity) I am very confused about what one 'Katal' actually is. From Wikipedia,

  "The katal is not used to express the rate of a reaction; that is expressed in units of concentration per second (or moles per liter per second). Rather, it is used to express catalytic activity which is a property of the catalyst. The katal is invariant of the measurement procedure, but the numerical quantity value is not and depends on the experimental conditions. Therefore, in order to define the quantity of a catalyst, the rate of conversion of a defined chemical reaction is specified as mols reacted per second. One katal of trypsin, for example, is that amount of trypsin which breaks a mole of peptide bonds per second under specified conditions."

So if a Katal is a specific AMOUNT of trypsin, then why is it expressed in units of moles per second. This is not dimensionally consistent! An 'amount' could be expressed as moles or mass, but certainly not as moles per second which is like a rate of reaction multiplied by volume...? The units and definition just seem to be all wrong.

If I were to take it that the Katal is the amount of enzyme catalysing one mole of a reaction per second, then this would mean that an enzyme with a smaller number of Katals of activity would actually be more active because less of it is required to catalyse one mole of the reaction per second?

A katal is indeed a specific amount of enzyme (rather than a reaction rate), but one which is measured with respect to the catalytic activity of the enzyme, rather than with respect to the number of molecules, their weight, or their size.

Roughly speaking, one katal is the amount of of enzyme which can convert 1 mole in 1 second. (Just like one pascal is the amount of pressure which applies one newton of force to an area of one square meter.) Or to rephrase things slightly, just like you can take an object of a particular length and express that length as "X meters" (being the number of meter sticks you can line up next to that length), you can take a given amount of enzyme and express the catalytic activity of that quantity of enzyme as "X katals", being the number of moles the enzyme can convert in one second.

This is not an intrinsic property of the enzyme itself. (It's an "extensive", not an "intensive" property.) The number of katals varies based on how much enzyme you have - if you have twice the amount of enzyme, you have twice the number of katals. (Just like you have twice the number of grams or twice the number of moles.)

As such, you can't talk about "an enzyme with a smaller number of katals of activity". I can understand the confusion, though, given the use of "activity" in the name. A paper the Wikipedia article references talks about the fact that there was some argument for calling the quantity being measured ‘catalytic amount’ rather than ‘catalytic activity’

As to why measuring enzyme amounts in katals versus moles or grams, the argument is similar to why there are separate units for mass (gram) and number (mole). It expresses a feature of the "size" of the enzyme not captured by the other units.


How is the site of administration of a vaccine decided? Vaccines can either be given intramuscular or subcutaneous or intradermal. I know the technique used is specific for each organism. What decides this?
I understand the reason for oral vaccines in polio but, why should a vaccine that is given s/c not be given im?

If there is a logic to this (which I am sure there is), it would be a lot easier to remember the same.

When the effectiveness of subcutaneous is comparable to intramuscular, then the choice is made based on the degree of discomfort and adverse reactions.

In many situations intramuscular will outperform subcutaneous delivery due to subcutaneous fat having poor vascularity which may result in slow mobilisation and processing of antigen(source).

Disclosure: I am not a biologist so this is outside my field of expertise.


Can I train my non-dominant hand and make it dominant? Are our dominant limbs decided on birth or is there some way in which I can train my non-dominant hand and make it as coordinated as my dominant?

Of course you can train yourself and make your non-dominant hand to be equal or even greater than your actual dominant handedness. Handedness is directly wired to the right/left hemisphere of your brain, so by training, you will actually re-wire your brain and acquire new pathways. It's a hard process in terms of breaking habits, otherwise, it's non-invasive and non-painfull, where most humans tend to give up before acquiring this skill justifying it as an unnecessary/low priority goal.

Handedness is not decided upon birth. It's gained in the earlier process (while a child is still in mother's womb) based on personal/individual preference (expressed by sucking a finger btw) toward right-handedness (90%) or left-handedness (9%), cross-dominance/ambidexterity (1%).

https://youtu.be/DU3OdTLuHf0
https://en.wikipedia.org/wiki/Handedness
https://ghr.nlm.nih.gov/primer/traits/handedness


Brain wave and motor movement correlation I am trying to better understand which brain waves are generated when the motor system (arms, legs, muscles of any kind) are activated.

According to Wikipedia, several types (Beta, Gamma, Mu) appear to be generated when motor movement is present, but it is not clear which muscle groups/movements/characteristics generate which types of waves.

Also, I see the certain waves (Alpha an Mu for instances) appear to have overlapping frequencies. If their frequencies are the same, then what makes them different?

As said by MG_MD:

  You would be thinking about moving, actually moving, and perceiving the movement. These affect different areas of the brain and as such, the electrical output would increase.

Also, it is very rare that the brain produces only one type of waves as it is continuously processing millions of information, though we know the basic functions of all of those types (from here).

As to how EEG works:

  The billions of nerve cells in your brain produce very small electrical signals that form patterns called brain waves. During an EEG, small electrodes and wires are attached to your head. The electrodes detect your brain waves and the EEG machine amplifies the signals and records them in a wave pattern on graph paper or a computer screen.

Source

Source of image

If you look at the image, th EEG has captured many waves of different types at the same time, which proves the staement of MG_MD.

For the "overlapping frequencies..." part:

  For example there is the “mu rhythm” (which is actually alpha activity in the relevant sensory and motor cortical areas that happens when the arms/hands are not doing anything)...

Source


Can fireflies species be identified with their wavelength? I was wondering if we could ID male fireflies using their wavelength? A bit like how we use UV light to ID species of scorpions.

In short: Yes it should be possible, but probably not for all species and as @anongoodnurse said there are probably easier methods of species-identification.

Elaboration:
I know (but could not find a reference) that there are currently hyperspectral cameras that are able to capture bandwidths as small as 2 nm.

And there are differences in the emission spectrum of fireflies.
Firefly luciferase bioluminescence color can vary between yellow-green (λmax = 550 nm) to red (λmax = 620). ( https://www.ncbi.nlm.nih.gov/pubmed/2801227 ) There are currently several different mechanisms describing how the structure of luciferase affects the emission spectrum of the photon and effectively the color of light emitted. (https://en.m.wikipedia.org/wiki/Luciferase)

However, it is likely that there are closely related species of firefly that have no (or very small) differences in emission spectrum. These will not be identifyable with spectral imaging.


What type of butterfly or moth is this? Can anyone please determine if this is a moth or butterfly and what its name? We found it near a waterfall in the Philippines. There's actually a bunch of them and it seems that it's their natural habitat which is close to the waterfall and a stream along.

That is a butterfly known as a "Mapwing". It is in the family Nymphalidae. I'm pretty sure it is Cyrestis maenalis. https://wikivividly.com/wiki/Cyrestis_maenalis


Does the human abdominal cavity use pressure to maintain posture? Several of my PT friends have referenced a physical therapist p who has studied breathing named Mary Massery. In her articles, she has referenced the idea of "intra-abdominal pressure"

http://www.masserypt.com/images/pdfs/Massery.%20Seating%20Symposium.%20Vancouver%202010.pdf

See page 2

If I am understanding her correctly, she is basically saying that

an unopened soda can is sealed and hard because of the pressure inside the canister
the human trunk tries to support itself upright. In this sense it is rigid. Therefore, it too must be using an internal pressure to create the rigidify necessary for uprightness. This is what she calls "intra-abdominal pressure."

My Question

Given what is known about the mechanics of human breathing, do the pressures of the abdominal cavity actually behave this way? Does the abdominal cavity rigidity itself using some sort of pressure? If so, how does this pressure mechanism relate to the mechanisms used during respiration?

If I am understanding her model correctly, I am extremely skeptical. A soda can is really not similar at all physically to the abdominal cavity.

I found this review which can help to clarify this notion of intra-abdominal pressure : Intensive Care Med. 2009 Jun;35(6):969-76.
What is normal intra-abdominal pressure and how is it affected by positioning, body mass and positive end-expiratory pressure?
De Keulenaer BL1, De Waele JJ, Powell B, Malbrain ML.
The authors mention that there is indeed a positive pressure in the normal subject. This IAP is contributed by gravity, uniform compression (abdominal contraction, diaphragmatic contraction, mechanical ventilation, rib cage excursions) and shear deformation, this last one depending on the intrinsic stabilty of the tissue.
The authors conclude that "the abdomen behaves as a hydraulic system with normal IAP of about 5–7 mmHg..". Kind of a can of soda, without the bubbles...
Pathologies affecting this pressure are named "abdominal compartment syndrome) and result from multiple etiologies (obesity, trauma...,).


Chimeric Gene vs Fusion Gene? According to wikipedia on chimeric genes:

  These mutations are distinct from fusion genes which merge whole gene
  sequences into a single reading frame and often retain their original
  functions.

I am not totally sure I understand the statement. My interpretation is that a fusion gene is caused by a translocation of DNA in a single gene; therefore, it "retains their original functions". This is different from a chimeric gene where DNA from two or more different genes are translocated to a new location to form a completely new gene.

Is my interpretation correct?

A chimeric gene is formed from fragments of other genes whereas a fusion gene is formed from the entirety of other genes. Often in the literature you'll see the term fusion gene used for both cases.


Why is exclusive breastfeeding recommended for 6 months only? The WHO recommends exclusive breastfeeding for the first 6 months of a child's life.

  Review of evidence has shown that, on a population basis, exclusive breastfeeding for 6 months is the optimal way of feeding infants. Thereafter infants should receive complementary foods with continued breastfeeding up to 2 years of age or beyond.

Their website mentions "review of evidence", but what is that evidence? Why 6 months and not 4 or 5 or 7 or 8 or 9 or anything like that?

Can anyone give which review is WHO talking about?

I guess this is the review (ISBN: 92 4 156211 0) that they are referring to.

  We found no objective evidence of a “weanling’s dilemma.” Infants who
  are exclusively breastfed for 6 months experience less morbidity from
  gastrointestinal infection than those who are mixed breastfed as of 3
  or 4 months, and no deficits have been demonstrated in growth among
  infants from either developing or developed countries who are
  exclusively breastfed for 6 months. Moreover, the mothers of such
  infants have more prolonged lactational amenorrhea. Although infants
  should still be managed individually so that insufficient growth or
  other adverse outcomes are not ignored and appropriate interventions
  are provided, the available evidence demonstrates no apparent risks in
  recommending, as public health policy, exclusive breastfeeding for the
  first6 months of life in both developing and developed country
  settings. Large randomized trials are recommended in both types of
  setting to rule out small adverse effects on growth and to confirm the
  reported health benefits of exclusive breastfeeding for 6 months.

However, another report suggests that exclusive breastfeeding for a long time may lead to deficiency of some nutrients which cannot be supplemented via maternal diet.

  The dual dependency on exogenous dietary sources and endogenous stores
  to meet requirements needs to be borne in mind particularly when
  assessing the adequacy of iron and zinc in human milk. Human milk,
  which is a poor source of iron and zinc, cannot be altered by maternal
  supplementation with these two nutrients. It is clear that the
  estimated iron requirements of infants cannot be met by human milk
  alone at any stage of infancy. The iron endowment at birth meets the
  iron needs of the breastfed infant in the first half of infancy,i.e. 0
  to 6 months. If an exogenous source of iron is not provided,
  exclusively breastfed infants are at risk of becoming iron deficient
  during the second half of infancy. Net zinc absorption from human milk
  falls short of zinc needs, which appear to be subsidized by prenatal
  stores.

Both these reviews are from WHO website; you can search for different WHO research materials on the site.

Note: WHO does not say that breastfeeding should not be continued till a later stage. As noted in the review, exclusive breastfeeding for more than six months can cause some nutritional deficiencies. However, reducing exclusive breastfeeding to 3-4 months can reduce the immunity of the infant.


What physical evidence exists that shows motor proteins "walking" within a cell? Various animations on the internet show the motor protein kinesin walking within a cell. Is this an approximation? How does this happen and (based upon what physical evidence) how do we know it "walks" like this?

https://www.youtube.com/watch?v=y-uuk4Pr2i8

http://imgur.com/gallery/WOTJdLp

https://www.youtube.com/watch?v=tMKlPDBRJ1E

Since you chose kinesins as an example class of motor proteins, I will also stick to them. In general, the movement mechanisms of kinesins are well studied and the general structure of kinesin proteins, that is a dimer, is known by crystallography (see Kull et al. (1996) for the structure publication).

Even before that, the movement of single kinesin molecules in discrete steps of approx. 8 nm was shown by Svoboda et al. (1993). To resolve single molecules, they used optical trapping interferometry (see this practical guide to optical trapping by the Princeton University for more detailed information). Four years later, Schnitzer and Block (1997) were able to show that that for every step of approx. 8 nm lof a kinesin molecule, one ATP is hydrolysed. Visscher et al. (1999) used molecular force clamps to study ATP and load dependent characteristics of single kinesin molecules.

So far, it appears to be that kinesins move by a 'hand-over-hand' mechanism: Yildiz et al. (2004) labelled single heads of kinesin dimer molecules with a fluorophore and found that their data are congruent with a step of approx. 17 nm followed by a step of approx. 0 nm which indicates that the two dimer hands alternate in movement.

See also the review by Hirokawa et al. (2009) for a general overview of kinesin movement.


What chemical test can be used to tell apart meat and plant-based meat? Long story short, I thought about this question and simple Google searches weren't enough. I know there must be some nutrient that can only be found in one of the meats but not the other, but I can't seem to search for it.

For this scenario, just assume that the 2 meats are exactly the same in terms of texture, color, consistency, taste, etc., to the point where only chemical tests can tell one apart from the other.

There are a lot of things you could test for.  The thing that come to mind off the top of my head is cholesterol.  This will be present in all animal meat, since all animals muscles contain cholesterol, whereas meat substitutes usually do not.
That said, there are other options as well (such as starch vs. glycogen levels, for example), and even molecules such as collagen differ between plants and animals, so a careful analysis (provided the proteins have not been too altered by the commercial production process) should be able to reveal thousands of differences, even in molecules found in both plants and animals.
Further reading

Marzetta CA, Rudel LL. 1986. A species comparison of low density lipoprotein heterogeneity in nonhuman primates fed atherogenic diets. Journal of Lipid Research.  27: pp. 753-762


What causes swelling after impact? Why does the head swell after getting hit by something hard? What is the liquid that forms after impact?

When physical damage to the cells occur a biological process called inflammation occurs. When inflammation occurs, white blood cells are rushed to the area in order to fight off any bacteria or harmful waste leakage from damaging the cells further. In order to get the white blood cells to the site of damage faster, the body induces a process called vasodialation where the arteries are expanded and blood is rushed to the site. This causes the site of injury to swell and redden, two signs of inflammation. The white puss that forms comes from the white blood cells. The white blood cells release chemicals that kill of bacteria and waste in the area and forms a white pus that will eventually harden or break through the skin to be exerted. If the site of impact begins swelling within a matter of hours, it is likely acute inflammation is occurring and the body is rushing blood to the site. However, if swelling occurs on a more rapid time scale it is more likely that this fluid is from the damage of the impact itself and the cells and capillaries are leaking blood and extracellular fluids (What is Swelling?).

In short, when you bump your head your body is trying to fight off further injury and infection by inducing the inflammatory response. It is also leaking fluids due to the impact and may result in rapid swelling at site of impact. The symptoms you discuss are due to inflammation and are a normal process of your body's defense mechanism. Hope this helps!


Where can I find the metabolic network for the human erythrocyte? Where can I find the metabolic network of the human erythrocyte (red blood cell), in SBML format? The red blood cell metabolic network is a model that's usually employed in the literature [see refs below] to demonstrate mathematical techniques of analysis of metabolic networks.

Despite this common use, I haven't been able to find a metabolic network of the human erythrocyte in SBML format, which is commonly employed for these networks (for example, in the BiGG database, http://bigg.ucsd.edu/) because it is easy to use with the COBRA package (http://opencobra.sourceforge.net/).

So, anyone can tell me where I can find an SBML model of the metabolic network of the human red blood cell?

References where the red blood cell metabolic network is used:

Wiback, S. J., Famili, I., Greenberg, H. J., & Palsson, B. Ø. (2004).
Monte Carlo sampling can be used to determine the size and shape of
the steady-state flux space. Journal of Theoretical Biology, 228,
437–447. doi:10.1016/j.jtbi.2004.02.006
Braunstein, A., Mulet, R., & Pagnani, A. (2008). Estimating the size
of the solution space of metabolic networks. BMC Bioinformatics, 9, 240. doi:10.1186/1471-2105-9-240
Jamshidi, N., Edwards, J. S., Fahland, T., Church, G. M., & Palsson,
B. Ø. (2001). Dynamic simulation of the human red blood cell
metabolic network. Bioinformatics, 17(3), 286–287.
Kauffman, K. J., Pajerowski, J. D., Jamshidi, N., Palsson, B. Ø., &
Edwards, J. S. (2002). Description and analysis of metabolic
connectivity and dynamics in the human red blood cell. Biophysical
Journal, 83(2), 646–662. doi:10.1016/S0006-3495(02)75198-9

The model used by Jamshidi et al. can be found in the BioModels database with acession no. MODEL1103210001  http://www.ebi.ac.uk/compneur-srv/biomodels-main/MODEL1103210001

A more recent model has also been described in Bordbar et al. iAB-RBC-283: A proteomically derived knowledge-base of erythrocyte metabolism that can be used to simulate its physiological and patho-physiological states. BMC Systems Biology 2011, 5:110 The model file in SBML format can be downloaded from the Additional Files section (http://www.biomedcentral.com/1752-0509/5/110/additional) or BioModels (http://www.ebi.ac.uk/compneur-srv/biomodels-main/MODEL1106080000).


Why were dinosaur skeletons so light compared to mammal skeletons? I was watching a presentation by Dr. Jessica Theodor [1] who discusses (at 38:10), among other things, the skeletal structure of dinosaurs vs. mammals. "Dinosaurs have way lighter skeletons, which means that for the amount of material they can be bigger. If we start to look at sauropods, they have this really interesting set of structures, these big holes in their vertabrae...
it allows you to build a lighter, stronger skeleton. Mammals can't do that. It's not how we build our bones."

Why don't mammals do this? Are there fundamental trade-offs that make our (apparently) weaker, heavier bones better, or is it just chance that we haven't matched this development?

(Of course I'm open to the possibility that I misunderstood the talk, or that it was simplified to the point of inaccuracy on this point.)

[1] Jessica Theodor, Being Giant: Why are mammals not as big as dinosaurs? (2015)

I have also heard the claim that dinosaur bones were lighter than mammal bones of equivalent  size, and at the moment I do not believe it.  I will not believe it until somebody explains it to me how that is possible.

If you have a structure that you want to add more weight to, to support that weight, you want to ADD structural elements, not subtract them.  If the structure could support itself before adding more weight, then adding structural elements will make it stronger (unless it's already at the absolute limit).  Otherwise, the structure does not stand at all.

If you google about the weight of bird bones, you can find recent research saying that bird bones are actually not lighter than mammal bones.  Their weight is just distributed differently (more densely on the outside of the bone, as opposed to more evenly spread throughout the bone as in mammals) to resist bending and twisting better at the cost of being weaker to impacts.  Birds arguably have a much stronger reason to lose weight than dinosaurs, but their bones are still just as heavy as ours.  Since birds are dinosaurs, I find it very unlikely that ancient terrestrial dinosaurs had magic bones lighter than both mammals and birds.

Also, I'm aware that the internal structure of our bones is very efficient.  As I understand it, the bone on the inside of a bone grows thicker where it is more stressed.  If you train a computer to calculate the ideal lattice structure to support the stresses of a given bone shape, the computer calculates pretty much the exact same lattice as what actually exists in our bones.  So, if the internal structure of our bones adapts to better handle the stresses we experience in life, and if the bones of vertebrates can evolve into any external shape whatever, I cannot imagine how dinosaur bones could be stronger than ours unless they were made of a different material.  I am not aware that this is the case.


What's the minimum distance of focus for the lens of a human eye to reach maximum flatness? According to the Wikipedia article on eye accomodation, the range in which a human eye can focus is from 7 centimetres away up to essentially an infinite distance. Of course, people can't see things an infinite distance away, but at a certain point the light reflected off an object will come at the eye in effectively parallel paths.

As an eye focuses on objects progressively farther away, it seems to me there would be a point when the lens hits maximum flatness, after which it everything will be equally sharp in focus. Looking at an object 500 metres away or 1000 metres away probably doesn't require any change in the lens. However, going from one metre away to seven requires the ciliary muscles adjust to just the right amount.

My question is, what is a normal minimum distance from the eye at which the lens will reach maximum flatness? Everything else in this question is just for context, so an answer to this, stated in metres from the eye, is all I am seeking.

The article I linked to above mentioned the human eye seeing "13 dioptres", and I have tried to understand dioptres, but it's a little confusing for me. If I understand correctly, the higher the dioptre, the closer you focus, so the 13 dioptres refers to how close the human eye can see. If I have this backwards, please let me know.

In any case, my purpose in asking is to determine the range in which ciliary muscles would be required to do more nuanced work in order to hold the lens at in the right shape. Focusing on something 7 centimetres away, the ciliary muscles are at maximum exertion, and at a certain point and beyond the ciliary muscles are completely relaxed. To hold somewhere in between would require more subtly nuanced, and, I suspect, more difficult work on the part of the ciliary muscles.

At least, I assume that to be the case because I am hypothesizing that the act of contraction for the ciliary muscles would be similar to other muscles. For example, it is easier to do a bicep curl with weight when going from full resting position to maximum contraction, as opposed to stopping at a particular spot somewhere in the middle of the motion. To stop mid-motion requires more muscle control, and, depending on how fast you wanted to do it, can be difficult to be exact.

There are practical questions in ophthalmology and you've asked someone that has a common theoretical answer: 6 meters.

However, you should know that from the same theoretical point the far the object the less accommodation we need, so the second answer is - infinity.

What is the difference? From the practical point the accommodation between this two points is negligible and does not have to be taken into account when we correct the refraction error.

Small theory - to see an object placed at a distance of 1 meter we need 1D of accommodation power (1/1meter=1D), to see an object placed at a distance of 30cm we need 3D of accommodation power (1/0.3meter=3D), for an object at a distance of 10cm we need 10 diopters and finally for an object at the distance of a 6 meter we need accommodate 0.16 diopter.

Thus between 6 meter and infinity the accommodation is very low and this is why the distant visual acuity is checked at this distance. Consequently, the lens convexity difference between 6 meters gaze and infinity is negligible and this is why the answer to your question is between 6 meters and infinity (zero accommodation).

From this explanation you can calculate the dioptric add for any reading distance  and understand how the reading spectacles correct the loss of accommodative power (=presbyopia, the vision of older people).

If you want to know how much the crystalline lens changes its dimensions during accommodation, the answer is near 7% for diameter and near 10% for thickness, so the lens as was convex, stays convex and the visible changes are minimal.


Is Race the Result of Microevolution I've been studying evolution for some time and was wondering whether the emergence of different races is an example of micro evolution within our species?
Bonus Question: is it impossible for homo sapiens to undergo to split into separate species via macro evolution?  I think it's impossible since were so interconnected (due to globalization and transportation), therefore speciation could not occur.

Thanks

Micro- and macro- evolution are terms vaguely referencing to arbitrary time scales

The terms microevolution and macroevolution have rather arbitrary and unclear meaning. For this reason, they are rarely used in the scientific literature. When they are being used, it is often in the first part of the introduction where general statements for which inaccuracy matters little are being made.

Typically, the existence of lineages called races (but see below) within a greater lineage called a species are limit cases between what one would want to call macro evolution or micro evolution. But in essence, it really does not matter where such arbitrary boundary is put, it changes nothing to evolutionary processes at play.

The concept of ethnic group

Note also that the concept of race (generally called ethnic group) is a human made concept that sometimes fail to match the reality of population structure in humans. If we were to name lineages based on genetic differentiation rather than socio-cultural cues, we would, if I am not mistaken, end up with a reasonably different result.

Bonus question

For your bonus question, you'll probably want to have a look at the post Does it make sense to classify all humans in a single species? and the post How could humans have interbred with Neanderthals if we're a different species? who discusses the concept of species.

You are right that the increased migration rate brought about by globalization causes increase interbreeding between humans lineages and will therefore rather prevent any further population structure that would have otherwise eventually lead to an event of speciation. There is, for the moment, no sign that any human speciation would evolve any reproductive barrier with any other human lineages. We are for the moment far from any speciation event in humans.


Free Radicals for aging From my understanding free radicals play a slight role in ageing.

In what ways are they so damaging, and can a restricted diet reduce production of free radicals?

Free radicals are damaging because their unpaired electrons (or not fully filled valence shell) makes them highly reactive species. They are often considered together with highly oxidizing "reactive oxygen species" (ROS) such as peroxides. They are especially problematic for cell membranes and DNA. In the latter they can react with (oxidize) heterocyclic bases.

As suggested first by Gerschmann et al. (1954), since oxidative damage to cells and cell structures is seen to accumulate with age, the corollary of this could be that aging is a result of oxidative damage. The very fact that cells have antoxidant enzymes such as superoxide dismutase (SOD) suggests that suppression of these species is important in the cell.

Many (but not all) ROS originate from mitochondria during cell metabolism. Therefore, it has been suggested that by regulating metabolism (that is, reducing the metabolic rate) the "rate of living theory" (Harman 1981) the rate of oxidative damage can be reduced. One way to do this may be calorie restriction.

This idea seems to fallen out of favour though. Another possibility is that the rate of mitochondrial ROS has nothing to do with metabolic rate per se; rather it might simply be a longevity determinant.

However, having said all this there is evidence that ROS are actually crucial in a number cellular pathways. It may be that it is the deregulation of pathways managing ROS that can contribute to aging rather than simply damage accumulation with age.

Gerschman, R., Gilbert, D. L., Nye, S. W., Dwyer, P., and Fenn, W. O. (1954). "Oxygen poisoning and x-irradiation: a mechanism in common." Science 119(3097):623-626.

Harman, D. (1981). "The aging process." Proc Natl Acad Sci U S A 78(11):7124-7128.


Can people be bred for tameness in a similar way to Russian foxes? Russian foxes were selectively bred for tameness. Can a similar process happen to humans, under the right conditions — say, extreme political pressure to obey ?

Setting aside the eugenic implications of what are you suggesting (short answer: yes it is theoretically possible, but no it is practically impossible), a more interesting observation is that evolutionary anthropologists think that humans might have "self-domesticated" during our evolutionary history.

There is a wide literature on this topic, but a recent paper summarizes the main ideas and addresses the question from a genomic point of view. Theofanopoulou and coauthors find credible genomic evidence for similar patterns of genetic evolution in humans and other domesticated animals.


Is there a family equivalent to "congener"? Is there an equivalent word to "congener" but for species in the same family (family in the sense of the taxonomic rank)?

"confamer"? "confamiler"???

I know I can just say "species X and other taxa in the same family" but I thought a nice one-worder would be better if anybody uses such a word.

Confamilial is the term for same family, it has even been used in print.

  Congenerics were twice as likely to fight as conspecifics, and confamilial competitors were three times as likely to fight as conspecifics.


Do effects of caffeine on human body change with habitual use? I've been reading about homeostatic nature of a lot of neurobiological processes - the brain is trying to maintain a balance by desensitizing receptors, re-uptaking and breaking down neurotransmitters.

With this in mind, I'm interested in what happens to the receptors in the brain with chronic use of caffeinated beverages.  Let's say an occasional caffeine drinker likes the cognitive boost of caffeine and starts to consume it habitually/chronically - every day. Will the caffeine drinker experience the same effects day after day, or will the effect change over time?

If there is a change in how the body responds to caffeine, are there any time frames that can be used to estimate when the change takes place - is it X days/weeks of habitual use?

Thank you for your input!

I don't have any references off hand (though if you like, I will find them). The body acclimates to caffeine intake, becoming desensitized to chronic caffeine use, analogous to chronic narcotic use. Habitual coffee drinkers, soda drinkers, and so forth must achieve the same level of daily caffeine intake to maintain a normal state of being. Taking in less caffeine leads to withdrawal symptoms, and taking in more caffeine leads to the familiar stimulatory effects. As for time frame of addiction, this likely varies, but I hazard a guess it's on the order of a few days to a week. Fortunately, caffeine is not nearly as strong and addictive as narcotics, however it is the most widespread.

Edit: Caffeine exerts high-affinity and low-specificity for adenosine receptors. This was a review article I fould that may help you out.

Dunwiddie TV, Masino SA. The role and regulation of adenosine in the central nervous system. Annu Rev Neurosci. 2001;24:31-55.


What is nastic movement due to growth? I have read in my biology book that

  "nastic movement is the movement that occur due to difference in the rate of growth on two opposite sides of a plant organ" ,

but I can't visualize how this movement take place and how the rate of growth cause this movement?

Think about say the left side of a shoot growing more than the right side. That way the left side will be longer and will be pulled back by the right side. This causes the shoot to turn to the right. By controlling the differences in the rates of growth in the two sides (using plant hormones) the plant can control exactly how much the shoot will turn.

Most nastic movements however, are not directional. For example, in Thigmonasty, or the movement due to touch, of the Mimosa pudica (or the touch-me-not), cells at the base of the leaves pump out K+ ions and Cl- ions, while taking in Ca+2 ions, thus create a osmotic gradient and lose water. This loss in water results in a drop in turgor pressure of the leaves and they droop.

https://en.wikipedia.org/wiki/Thigmonasty#Thigmonasty_in_the_Fabaceae


SNPs mapping into protein Starting a new project on protein-protein interactions and SNP analysis tool development. I would like to ask how does SNPs is mapped into protein? What does mapping means?

Well SNPs are single nucleotide polymorphisms. Some SNPs are in the coding regions of genes and they can result in changes in the resulting protein. For example, the SNP rs1801131 is a human variation where some individuals have a G instead of an A at position 1515 of the gene MTHFR. When the gene is transcribed and then translated into protein, this variation (the presence of the G nucleotide) causes a Glutamate residue at position 429 of the protein to be a Glycine instead.

So, SNP rs1801131 maps to position 429 of the protein MTHFR.


What do bloodsucking animals actually feed on? A number of animals, including mosquitos, leeches, ticks and so on, feed on blood. And yet, at least in mammals, most stored nutrients can be found in body fat as fat, muscles and liver as glycogen and digestive system as undigested nutrients, leaving very little in the blood itself. Normal blood sugar before a meal is 70-99 mg/dL, which at the high end means blood contains roughly 3.8 kilocalories per liter. This means that to gather a single kilocalorie from blood glucose, it would take 26 mL of blood, more than any leech could reasonably hold. Estimating the mass of a leech at 20g and scaling down human caloric needs linearly, 2500 kilocalories per 70 kg, yields a leech caloric requirement of 0.714 kilocalories per day. By this estimation, a leech would need to feed at least once per day to meet its energy needs, and yet data from the American Museum of Natural History states that a leech need only feed once every few months. The same math holds for other bloodsucking animals.

So what in blood do bloodsucking animals actually feed on?

Lets find out how much calories are there in the blood. I am using this site for main reference, but will also add more references where needed. But before that, we should know that one donation of blood is about 1 pint (or 450 ml) blood1. But here, I calculate with volume 500 ml.

First calculate calories for plasma. Blood is denser than water by six percent2, so multiply that 500 ml donation times 1.06 to get to grams (because calorie content will be calculated from grams). Multiply that by 55/100 for men or 60/100 for women to get to grams of plasma. Now, multiply that by .07, because plasma is only 7% protein3, to get to grams of protein. Finally, multiply that result by four to get protein calories. Here, considering 55/100, I get 81.62 calories.
Now for sugar in plasma. Normal fasting blood sugar is around 0.09 grams per 100 ml of plasma (more familiarly expressed as 90 mg/dl4). Multiply the amount in grams time 2.75 for men or 3.00 for women, i.e., equal to how many hundreds of mls of plasma there are in 500 ml of blood, and then times four to get to calories. Result should be 1 calorie.
For plasma calories from fat, use 0.5 grams per 100 ml5 of plasma, times hundreds of mls of plasma, times nine - for calories from grams of fat - to get to calories.  Result is roughly 12 calories.
Next comes calories from red blood cells. RBCs are mostly water and protein, the protein almost entirely hemoglobin. Hemoglobin does not conform to the rule of four calories per gram because the heme portion of the molecule is not metabolized for energy. Use average hemoglobin values of 160 g/L for men or 140 g/L for women6, multiplied by 0.5 to get to the blood donation volume of 500 ml, multiplied by 0.96 to correct for using only the non-caloric heme portion of the hemoglobin molecules, then multiplied by four to get to calories. Hemoglobin is only 90% of the dry weight of RBCs7. Multiply one-tenth the amount of the hemoglobin weight in 500 ml times six (see below for why six) and add that to red blood cell calories. I get 353.28 here.
Finally, estimate calories for the other types of cells. Of the 500 ml blood donation, roughly one percent will be white blood cells and platelets8. Figure five grams, times one-third to get to dry weight, times six, to get to an estimated 10 calories. The "times six" is because some of the dry weight is protein or carbohydrates, which both have four calories per gram, and some is fat, which is 9 calories per gram.

Add everything up. The total should be approximately 425 calories for women and 460 for men in 500 ml blood i.e. even 10 ml of a man's blood contains about 9.2 kcal (there's no definite answer about how much blood a leech drinks at a time). Now, as you say in your question that a leech requires about 0.714 kcal, it means that a leech can survive for almost 13 days by sucking just 10 ml of a man's blood (if they have to metabolize everything present in blood (except, of course, water)), which justifies your statement.


Does the string "...CATCAT..." appear in the DNA of Felis catus? In Hofstadter's Gödel, Escher, Bach: An Eternal Golden Braid (GEB), the following claim appears:

...in the species Felis catus, deep probing has revealed that it is indeed possible to read the phenotype directly off the genotype. The reader will perhaps better appreciate this remarkable fact after directly examining the following typical section of the DNA of Felis catus:
...CATCATCATCATCATCATCAT...(OP note: truncated because, you get it)

Is this true? A cursory search for the DNA of Felis catus gives me this 1996 paper by Lopez, Cevario, and O'Brien and the given sequence does not appear – there are some instances of "CAT" but not repeated enough to make it as remarkable as claimed in GEB.
I don't know enough Biology to judge the veracity of this claim. Some points I am considering are:

GEB is full of wordplays. However, the tone of this part of the text does not sound like one to me.
GEB was written/published around 1978. The paper I linked to – which was cited by some 236 others according to Google – was published in 1996, way after GEB's time. If my impression that Lopez et al.'s work is significant because it is the first time Felis catus has been sequenced, then there is no way Hofstadter could've known of it when he wrote GEB. Then again, I don't know enough Biology that there might be some nuance to Lopez et al.'s paper that I'm missing (i.e., the results of the paper might not be mutually exclusive to the claim made in GEB).
GEB has reference notes and bibliography and there is no reference cited to back this claim. However, GEB does not attempt to be a rigorous academic thesis and the references is only called upon more when Hofstadter quotes other works directly while the bibliography is a list of readings which the reader may want to check out, regarding the main thesis of the book.

So are cats recursions with no base cases?

The Felis catus genome has been published, annotated, and updated quite a bit since 1996, including spans of so-called intergenic regions, which are basically scaffolding and other structures, along with perhaps some unidentified genes, pseudogenes, regulatory sequences, etc. Basically, pretty much the entire DNA sequence is available now, not just the gene sequence of the mitochondrial genome, which was what was published in the 1996 paper you referenced. Mitochondria are the power plants of the cell, but are just an organelle that happens to contain its own DNA; they are separate from the chromosomal DNA in the nucleus. All of this is available for free (if you know where to look) at the National Center for Biotechnology Information (NCBI), part of the National Library of Medicine (NLM) at the National Institutes of Health (NIH) in the United States. Other sites are also available, such as Ensembl, a joint project between the European Bioinformatics Institute (EMBL-EBI), part of the European Molecular Biology Laboratory (EMBL), and the Wellcome Trust Sanger Institute (WTSI). Both institutes are located on the Wellcome Trust Genome Campus in the United Kingdom.
So, to the genome. Genomic sequences can be searched in a couple of different ways, depending on what you're looking for, but the most common way is to use BLAST, the Basic Local Alignment and Search Tool. As the name implies, it takes sequences as input and searches one against the other, aligning the results as best as possible using certain algorithms that the user can define and tweak. The BLAST web interface to the cat genome is here. You don't need to worry about any of the other options here except the "Enter Query Sequence" box. FASTA format is just using the single-letter abbreviations for nucleotides (AGCT), all strung together.
The genome we're searching is of an Abyssinian cat named Cinnamon:

Cinnamon, the cat which was chosen to be the definitive genetic model for all cats in the feline genome project. Image courtesy of the College of Veterinary Medicine at the University of Missouri.
To start with, I typed in CATCATCATCAT and to my surprise got back over 200 hits, covering every chromosome the cat has. So, I doubled the length of the input to 8 CATs, and got back the same result set. Unfortunately, 12 CATs was too many (and really, it is too many), so I worked backwards.
The final results are here (sorry, link expires 10/13/16. To regenerate, go to BLAST link above and enter CATCATCATCATCATCATCATCATCATCAT). Apparently, popular wisdom is incorrect, and Felis catus chromosomes really contain 10 CATs each, one more than is needed for their 9 lives. No word yet as to why this may be, but scientists are presumably working on it.


How does hibernation reduce risk of radiation-induced mutation? A recent documentary (skip to 58:20) discusses the possibility that hibernation, if it could be induced in extrasolar astronauts, would reduce damage from cosmic radiation. The obvious reason this could happen is the shielding of hibernation chambers, but the documentary reviews evidence that even hibernation in the wild (e.g. bears) reduces radiation damage due to a slowed metabolism.

I would assume the connection is that reduced need for enzyme synthesis keeps DNA coiled up most of the time so its nucleotides are less exposed to radiation, but even if this is true it raises the question of how coiling shields radiation. (For example, is it less able to penetrate histones or the phosphorylated deoxyribose backbone?) Adding to my confusion, the documentary claims the mechanism is rooted in hydrogen sulphide, but doesn't explain either why this is more concentrated in the cells of hibernating animals nor how it reduces mutations.

This is still an area of active research, and there doesn't appear to be a single definitive answer for the mechanisms behind the reduction in radiation-damage during hibernation.
A recent review by Cerri et al. (2016) covers a lot of the known biology behind hibernation and resistance to radiation damage.
A few select quotes from this review:

At the cellular level, it is well known that cells irradiated in
resting state, and left undisturbed for 24 h after irradiation, are
more resistant than cells re-plated immediately after exposure. This
effect is known as delayed plating, and is generally attributed to the
potentially lethal damage repair (PLDR) in resting phase.
...
The oxygen level during hibernation may contribute to the enhanced
radioresistance. Hypoxia is a well know protective mechanism, and is
arguably the main reason of local control failure in radiotherapy.

Rockwell et al. (2009) discuss the underlying reason behind reduced radiation sensitivity in a hypoxic environment:

Molecular oxygen (O2) is a potent chemical radiosensitizer. This
radiosensitization does not result from any of the metabolic or
physiological effects of oxygen, but instead reflects the fact that O2
is an extremely electron-affinic molecule that participates in the
chemical reactions that lead to the production of DNA damage after the
absorption of energy from ionizing radiation [21,22].

My personal take would be that the reduced risk of radiation-induced damage is probably not due to the structural arrangement of DNA, but rather the overall cellular environment. This is perhaps linked to an enhanced ability to repair damaged DNA, but is also likely to be highly dependent on cellular oxygen levels.


What does "rapamycin-sensitive oncogenic transformation" mean? Can someone explain exactly what "rapamycin-sensitive oncogenic transformation" is? I get that it's a drug that suppresses the immune system but what does it have to do with oncogenic transformation?

Here's the article where they talk about it:

http://www.pnas.org/content/104/13/5569.full

The mammalian target of rapamycin (mTOR) is a Ser/Thr protein kinase that functions as an ATP and amino acid sensor to balance nutrient availability and cell growth. When sufficient nutrients are available, mTOR responds to a phosphatidic acid-mediated signal to transmit a positive signal to p70 S6 kinase and participate in the inactivation of the eIF4E inhibitor, 4E-BP1. These events result in the translation of specific mRNA subpopulations. mTOR is phosphorylated via the PI3 kinase/Akt signaling pathway and also autophosphorylates under translationally repressive conditions. mTOR plays a key role in cell growth and homeostasis and may be abnormally regulated in tumors. It is currently under investigation as a potential target for anti-cancer therapy.

The mTOR signaling pathway shows how mTOR is involved in numerous cell processes that can be dysregulated in cancer, including cell growth, proliferation, angiogenesis, autophagy, and various kinds of metabolism. "Rapamycin-sensitive oncogenic transformation" therefore means that the transformed cells still have intact "wild-type" mTOR complexes that can be down-regulated by the tumor-specific administration of rapamycin analogues, hence inhibiting the above-mentioned processes and arresting or killing the cells.


Regarding plant stress I have to plan a bioinformatic study on a plant. Microarray data is available for various stress treatments (drought, cold, osmotic and flood stress) on root and shoot tissues. I am a bit confused as to which tissue is more important for the perception of stress and its direct effect. I want to start with one of them as of now, since the study will get too complicated with so many stress conditions and tissues. I am not from a botany field and look for some thoughts. Sorry if my question sounds silly.Thanks a lot.

I know this is not what you want to hear back, but I think you should go with all the samples/replicates at once. Only this way you will have the highest possible statistical power to claim the results that (hopefully) you'll have in the end.

When it comes to microarrays and RNASeq, also, it is important to remember that these are mostly whole-transcriptome techniques, therefore the way they are thought to be used is more like "sequence all > analyze all > fish for specifics" than the opposite.

I would use all of them, feed them to a proper pipeline (there are many, not my duty to suggest you one) and see what has a good score/p-value. If you had something in mind before doing the microarrays you probably would have assessed only a subset of the genes, and not the whole transcriptome. So go for both tissues and see what pops out!


Which is more important for protein expression mRNA structure or codon optimization? The field seems extremely divided on the debate. On one hand, artificial experiments have suggested that synonymous mutations don't correlate with gene expression but rather, the mRNA 5' structure is the most important 1. On the other hand, genome wide analysis suggests that tRNA biases are better associated with high expression 2. What other works balance out this discussion?

Coding-sequence determinants of gene expression in Escherichia coli
Translation efficiency is determined by both codon bias and folding energy
An evolutionarily conserved mechanism for controlling the efficiency of protein translation

This is an excellent question! To my knowledge, there hasn't been a definite answer yet. Recently, I did tons of research on which factors influence protein expression and you should definitely check out the following questions which I asked:

What is the criticality of the ribosome binding site relative to the start codon in prokaryotic translation?
What determines a successful protein expression in E. coli?

I answered my second question by posting a concise version of a paper from DNA2.0 (a gene synthesis company) that discusses the protein expression. It summarizes all the important factors (RBS site, codon frequency match, 5' mRNA secondary structure), but it doesn't discuss the extend to which they influence expression.

There is a nature paper from Voigt lab about RBS calculator, which takes into account only the 5' mRNA secondary structure and it doesn't discuss at all the codon-optimization. The calculator was good, but far away from perfect: there is a 50% chance of predicting an expression level within a 2-fold range of the target one.

On the other hand, an older paper from DNA2.0 argues that the mRNA is covered with ribosomes practically all the time, so the secondary structure of the mRNA should have little effect. Besides, an actively translating ribosome can break up stem-loop structures.

In my opinion, we are still far off from predicting RNA secondary structure formation, although it might be highly implicated in protein expression. From what I read, I think that it is equally crucial that there is no strong secondary structure at the 5' end of the mRNA, the RBS sequence is close to the consensus one and it it appropriately spaced upstream of the start codon, and the first 60-100 codon frequencies match the frequency of your heterologous host.


Looking to understand the difference between (Fibroblast Growth Factor) FGF-2 and FGF-5 Non-biologist nor medically trained person here, but still nonetheless interested in the functioning of the human body, and more specifically, hair growth cycles.
I've read in several sources that FGF-2 is potentially a hair growth 'stimulant' (source), whereas FGF-5 is a potential hair growth inhibitor (source) and I was looking to better understand the differences between the two?
According to a basic definition, and the bounds of my current knowledge, FGF's are signalling proteins that are involved in a whole host of bodily functions including but not limited to wound healing.
What are the potential differences between '2 and '5 that makes them appear to affect hair in opposite ways, as I would have thought that the general FGF family would act in a similar way if anything.

I'd suggest looking at this article on the FGF family. You will find a lot of information there about comparative analysis of the different proteins therein. For example (FGFR = FGF receptor, which binds FGF to transmit signals):

FGF–FGFR binding specificity is regulated both by primary sequence differences between the 18 FGFs and the 7 main FGFRs (FGFR1b, FGFR1c, FGFR2b, FGFR2c, FGFR3b, FGFR3c and FGFR4) and by temporal and spatial expression patterns of FGFs, FGFRs and HSGAGs. The alternative splice isoforms of FGFRs are generally tissue specific: the b isoform is usually expressed in epithelial tissue, whereas the c isoform is usually expressed in mesenchymal tissue23. Ligands are produced in either epithelial or mesenchymal tissue and generally activate receptors of the opposite tissue specificity: in normal physiology, a ligand produced in the epithelium will activate a mesenchymal receptor and vice versa. Several ligands, including FGF1 in particular, pose an exception to this general understanding by promiscuously binding to both b and c isoforms of certain FGFRs. Pathological states can result from a breakdown in binding specificity, as is common in cancers in which FGFs are overexpressed24. Structural studies of FGF1, FGF2, FGF8 and FGF10 with their cognate FGFRs show that sequence diversity at FGF N termini, variation in β1 strand length (FIG. 1b) and the alternatively spliced regions in D3 dictate their binding specificities (FIG. 2b, c).

So it's rather complex. Differences in FGF function are at least in part due to small biochemical differences that may give them differential affinity for different FGFRs, which then go on to transmit the FGF signals down the line. But at the same time the FGFs/FGFRs are expressed in different tissues, meaning that they may have relatively narrow spheres of influence.
If you look here you will see that different FGFs actually have relatively low similarity at the amino acid sequence level, and in some cases quite significant differences in gene structure (though they don't talk about 2 and 5 specifically). One notable difference there:

Most FGFs (FGFs 3-8, 10, 15, 17-19, and 21-23) have amino-terminal signal peptides and are readily secreted from cells. FGFs 9, 16 and 20 lack an obvious amino-terminal signal peptide but are nevertheless secreted [25,26,27]. FGF1 and FGF2 also lack signal sequences, but, unlike FGF9, are not secreted; they can, however, be found on the cell surface and within the extracellular matrix.

For some work on this topic specifically targeted towards FGF2 and FGF5, you can see this paper, which has this table about the location of FGF expression in follicle cells, showing that they are expressed in different places:

apologies to people with screen readers, I didn't have the motivation to copy it out into text. Here is a summary figure that they give:


Is there really a clear distinction between dinosaurs and birds? Traditionally, birds are classified as a class of dinosaurs and the term non-avian dinosaurs is introduced to refer to the rest.

As recent discoveries suggest that some dinosaurs may have been warm-blooded and that some dinosaurs had feathers, the distinction between birds and dinosaurs seems blurred.

I have often heard statements like "Birds are the only dinosaurs that survived the Cretaceous–Paleogene extinction event.". With recent discoveries, isn't this how the clade of birds is defined rather than a fact about the extinction?

// not sure if this question belongs in biology, sorry

The placement of the bird clade within the dinosaur clade is based on much more than just "having feathers and being warm-blooded"; paleontologists have discovered many, many ancient bird and theropod fossils, and as a result their understanding of what the theropod clade was like overall and how the bird clade developed within it is precise enough that discovering another group of dinosaurs was warm-blooded or even had feathers won't result in the conclusion "wow that dinosaur was closer to birds than we thought", but "wow feathers were a much more common feature among dinosaurs than we thought".

If you look at the Wikipedia page you can see there are many "bird-related" clade names that cover different levels of similarity to modern birds. From "Neornithes", which is defined as the clade containing all modern birds, to "Paraves", defined as the group containing all organisms closer to modern birds than to Oviraptors, which are all within Maniraptorans, which is itself pretty deeply nested within the Theropod clade...

So basically what I am trying to say is, our understanding of where birds fit within Dinosauria is precise enough at this point that no discovery about a single trait is going to "blur the distinction between bird and dinosaur"; it might change our idea of dinosaurs in general to be more bird-like, meaning that traits we thought were bird innovations might have been standard-issue in dinosaurs for a long time before, but it will not necessarily change our whole understanding of how birds and dinosaurs are related.

As for this :

  With recent discoveries, isn't this the definition of what a bird is rather than a fact about the extinction?

It isn't; the paleontological definition of what a bird is is not at this point an ad-hoc definition related to "whatever survived the K/Pg extinction". Even Neornithes, the crown group of all living birds, originates to before the K/Pg extinction. For example, the splits between ostriches and other birds and within that latter group, of ducks and geese from other birds are thought to have happened during the Cretaceous. And there are some researchers who argue that a few fossils indicate that some non-avian dinosaurs survived the extinction; the consensus view is that those fossils are dated wrong, but that this position exists shows that "non-avian dinosaurs went extinct at the K/Pg boundary" is a fact-based question, not a definitional one.


Effect of zero selection (pressure) on the population health Evolution naturally produces better features: stronger muscles, teeth and minds. Killing the weakest, evolution wipes defective genes out of populations.

The mutations are necessary for advance. However, they are random and, thus, mostly negative. Right? How does the nature eliminate them from the population?

I see that one mechanism is polygamy: male have higher mutation rates. They tend to reproduce as much as possible. Female have lower mutation rates, they couple with only with best men and contribute much more to their offsprings. So, men generate as much random solutions as possible, whereas the role of female is to conserve the best of them. This means that the most of the male (bad mutations) die unreproduced. This eliminates the bad mutations and favours the progress of good qualities. The higher animals started to form harems and tournaments over their ownership. This further fosters the elimination of weak men and profileration of strong genes. However, human monogamy has disabled this selection mechanism. Best men are dedicated to only one woman. Other women cannot mix their genes with other good genes from previous generations. They are forced to look at the low quality men, who carry degenerate mutations. Might be it is monogamy that makes us human but it implies that all genes reproduce.

Yet 100 years ago it was not a big deal since we still had another filter: our grandfathers were born in families that had normally 10 children (I am speaking about Russia) and only 2-3 survived until reproduction (the population increased really slowly). I bet that those who survived had really good health: thanks to the bad health and immense selection pressure, the negative mutants are eliminated immediately and population maintains a perfect genome (aka biologic health). Killing more weakest in the current generation improves the health of next generations.

However everything has changed during the 20th century. The advances in economy and medicine have almost eliminated the selection. The selection pressure has relaxed to essentially zero so that everybody survives and leaves the same amount of offspring (and some scientists are even concerned that degradatory individuals leave more offsprings than the prosperous ones). We have even eliminated the infant mortality. We use baby incubators so that the people with the weakest health could survive and reproduce as normal and we are proud of it. It may sound strange but the mutation rate has not changed at all. Does it mean that the human genome is in danger?

I see the situation like you have inherited a perfect mechanism and decided not recovering it from the inevitably adverse action of entropy, that degrades it constantly. There is a constant chance, d, that every good gene is affected by a mutation. It is a fraction of healthy genes that will fail passing to the next generation. This will leave only (1-d) genes healthy in the next generation. The fraction of healthy genes will melt like 1, (1-d), (1-d)², (1-d)³, an so on, with every generation.

You see the fraction that stays healthy over generations. It decays exponentially. Any utility turns into entropy (aka garbage) exponentially, if not protected. Is this model correct? How quickly does this dissipation go? What is d? Let's assume absolute survival and equality in the reproduction rate among all groups people. How many generations is needed to lose 50% of good qualities?

I need to point out one thing, natural selection does not bring species to perfection.  The best mutant may not be selected for many reasons.

When you have no selection pressure then you have neutral evolution concurring and what takes over instead of natural selection is genetic drift.  Genetic drift is just sample error.  Say you have 1,000 individuals in a population and all of those individuals reproduce, in the next generation all the genotypes would be in the next population.  Now imagine if you only had 10 individuals in the population and only 5 of those individuals were randomly selected to produce 10 individuals in the next generation (the parents die every year).  There is no selection pressure but just by chance some individuals reproduce and some don't.  If you do this over and over again what you will see is that some genes become fixed in the population, meaning that there is no other genotype in the population.

This fixation at small population sizes can occur with either beneficial or deleterious mutations.  Obviously if a mutation is very deleterious the individual will die but slightly deleterious mutations can become fixed in the population as well.

There is an entire field of biology devoted to this study.  It is called population genetics.  The probability for fixation for an allele is its proportion in the population.  This proportion can be calculated by 1/2N, where N is the population size.


Why don't we feel hungry after waking up? Yesterday, I was fasting (drinking only water until I had dinner at 9 pm). After dinner, I went back to my lab (I am a Master's student) and worked till 1:30 AM. By 1 o' clock, I was feeling quite hungry, probably because I hadn't eaten anything all day and only had a light meal for dinner. However, I didn't eat anything then and just slept. Today morning I wake up (around 9 AM) and I don't feel hungry! I could surely eat something if I wanted, but I am not feeling the acute hunger that I was feeling last night!

More generally, what could be the reason for the behavior that a human experiences acute hunger, but after sleeping for an extended period of time, he/she may no longer have the hunger. Since a passage of time has passed, one would expect the hunger to increase, which would have certainly happened if the person had not slept. Is it the case that sleeping somehow affects the overall hunger/glucose demands of the body?

I suspect that it is possible that the body's food needs could be majorly affected by the circadian clock, but I wanted an explanation to contrast the situation when one is not hungry and when one is very hungry before sleep. How can the difference between both the situations be easily trumped by the circadian rhythm's effect? (if it is the explanation!)

I will try to keep the answer as simple as possible, but feel free to point out if I make this too simple.

Well, you are not alone with this observation. This is quite a common, but rather complex, phenomenon which controls our apetite and causes us to not feel hungry after waking up.

The feeling of being hungry is under constant regulation by two antagonistic (having opposite effects) hormones:

leptin, released from adipose tissue, decreases our apetite and suppresses our hunger
ghrelin, released from stomach, does just the opoosite i.e. increases our hunger.

And guess what, these hormones are controlled through the circadian cycle. When you sleep, your body produces more leptin and stops the production of ghrelin. Why? The answer is quite obvious: because you're sleeping. While sleeping, your metabolism is lowered because your body needs to repair the damaged cells and tissues. To control metabolism, we need to control our apetite, and to control our apetite, we need to suppress our hunger. So...? When you wake up, you still have a hangover of this effect. In other words, it takes some time to change the secretion rates of leptin and ghrelin and the resulting effects.

Lets get into some analytical details now. According to Sharma et al, 2010, metabolic rate and brain temperature are lowered during non-REM sleep to deal with the damages that may have occured during time of wakefulness. In their study, the subjects were deprived of sleep for 2 nights (4 hours per night) and then allowed to sleep for next 2 nights (10 hours per night). The result? Leptin levels decreased by 18% and ghrelin levels increased by 28%. The subjects also craved for more carbs. Also, craving for salty foods increased by 45%. Overall hunger increased by 23% due to reduction in leptin levels. They also showed that people who sleep less than 5 hours have increased Body Mass Index (BMI). All this points to the fact that sleep does cause reduction in apetite and hunger. In short, don't think of missing your breakfast.

References:

Sharma, Sunil; Kavuru, Mani (2 August 2010). "Sleep and Metabolism: Overview". International Journal of Endocrinology. 2010: 1–12. doi:10.1155/2010/270832.
Wikipedia contributors. "Sleep and metabolism." Wikipedia, The Free Encyclopedia. Wikipedia, The Free Encyclopedia, 8 Feb. 2017. Web. 26 May. 2017.