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


How can potassium rich foods reduce blood pressure? How come sodium increases blood pressure, but potassium, which has to some extent similar properties helps lower it?

potassium is really the main guy in charge of everything that happens involving action potentials which in turn govern homeostasis such as blood pressure.

k+ lowers blood pressure due to making it harder to get an action potential going, which in the macro scale causes the heart to pump less.

too much k+ kills the person as it stops the pumping of blood (lethal injections are just lots and lots of k+ along with some pain killing drugs)


Help identify this awesome climbing plant with velcro like stem I got this plant sprouting in my window box this spring. Starting from a single seed, it has grown into an impressive array of branching climbing vines, reaching 6 feet tall. The stem turned red as it matured. The most awesome feature of this plant is that the stem is covered in micro hooks that cling to everything. I've seen it cling to a paint on a metal gutter pipe I can think of these hooks as velcro or gecko feet.

Can someone help me identify this plant?

climbing vine
stem is covered in tiny hooks that are very clingy
grows to 6 feet tall
stem turns to red as it matures
segmented leaves
leaves grow to palm size
new leaves sprout from stem where old leaves were connected
 -

I think this might be Japanese hops. Well, what I have in my yard is Japanese hops.

As I said, it's horrible.
Description and Biology:

Plant: herbaceous annual, twining, shallow-rooted vine that can climb to heights of ten or more feet with the help of rough-textured stems covered with short, sharp, downward pointing prickles that can be very irritating to the skin.

Leaves: leaves are rough-textured, paired, simple, palmate (like a hand) with typically 5-7 lobes; leaf margins are toothed.

Flowers, fruits and seeds: flowering occurs in July and August; male and female flowers are borne on separate plants; male flowers are very small, greenish yellow and occur in branched panicles; female flowers are in pale green, plump, drooping, cone-like structures with overlapping scales that become ‘hops’; hop scales and the seeds are covered with yellow glands; seeds are about 1/8 in. in diameter, roundish with a blunt tip, and light brown with darker specks; seeds mature through September.

Spreads: by seed which begins to germinate in early spring, but new plants may continue to emerge as the season progresses if sunlight and moisture are available; seeds are dispersed by animals (including people), machinery and floodwaters.

Look-alikes: native common hop (Humulus lupulus) looks very much like Japanese hop but it is usually 3-lobed or unlobed; native bur cucumber (Sicyos angulatus) lacks prickles, has tendrils, and the leaves have much less pronounced lobes.

Prevention and Control: Do not purchase, plant or transplant this species.

The Velcro Vine, known variously as Cleavers, Goose Grass and Bedstraw is botanically known as Galium aparine. New spring growth can be juiced or eaten in salads or on sandwiches. It can be used to stimulate and decongest  the lymphatic system and as a diuretic to remove excess H2O.


What processes regulate the sex of offspring? It is known that some species are more likely to born male than female (and some maybe vice versa). I understand that it is due to evolutionary perspective (average number of adult males is close to that of females), I want to know about how it is regulated.

What I thought is that spermatozoa are made by half as Y and half as X chromosome. Then mitosis and meiosis and the probability that one of them will die is equal for both types. So, somewhere I feel lost.

Also, can it be regulated by female body or not? According to this paper claiming that hormone levels in women affect the likelyhood to born son. Possibly it is just because they choose males that are more likely to have more Y spermatozoa than X, but if it is some chemical mechanism to regulate that I'd like to know.

I'm not asking only about humans, mechanisms can be similar in almost all mammals. I'm not asking about other species: I know some are regulated by temperature, etc. This question is only about mammals.

In theory spermatozoa are indeed produced in a 50:50 X:Y ratio. However, there are factors which can change the ratio, such as hormone-disrupting agents or even food.

Best known factor in the female body is timing. There are different theories of which The Shettles method is the most well known I think. In this theory they think that boy sperm are faster than girl sperm, but don't live longer. So to have sex around the date of ovulation highers the chance of getting a boy (their sperm is faster), but for a girl sex should be planned a few days before ovulation (they live longer). It is all theory, of course, so there are no guaranties.

Both can play a factor across mammalia.In humans it is difficult to study effectively (we can't lock people and cages and mate them in controlled patterns, nor will most parents volunteer to hormone injections for their fetus)  So we have less data on humans than for other species.

In other mammals we have had more luck and a variety of mechanisms exist, often several competing mechanisms withing the same species even.  Not surprising if you think about out what gender the males genes "wants" and what ratio the females genes want will not always coincide. In rats for instance the R2D2 gene (I shit you not) prevents female offspring by preferentially differentiating germ cells so only those that carry it become sperm. The gene sits on the Y chromosome so it is selfishly passing itself on at the cost of often wiping out populations becasue they have no females. this is the most extreme mechanism know but it illustrates the sheer variety that exist.

dominance and stress are often good predictive factors, while known mechanisms include Hormones driven differential implantation, differential ova production, differential spermatozoa formation, and differential sperm survival. More mechanisms almost certainly exist but the search for them is relatively new so it is not surprising most studies will list them as potential influences.

Many mechanisms actually makes sense evolutionarily speaking, since there are several competing factors preferring one sex or the other as far as the parents genes are concerned. For instance if the ratios get too far away from the normal ratios it creates a n increasingly strong advantage to produce offspring of the sex in the minority. Another factor is parenting style of the species, in more or less monogamous species the sex has little impact while if you are a species that has harems females are sure thing with low pay off (numbers of offspring) while males are high risk high reward, low chance of reproduce but those that do have LOTS of offspring. Even things like for genes on the Y chromosome every female is a failure is a factor. You mist also consider that chromosome profile is not the only controlling factor, sex phenotypes that do not match their genotype is surprisingly common in mammalian.

Source


Why are sponges sometimes not considered multicellular? I read somewhere (I can't find where) that there is no scientific consensus whether sponges should be considered multicellular organisms.

It seems I don't understand where is the line between unicellular and multicellular life.

I am not able to find a more elaborate explanation of that doubt. What are the reasons for it?

Sponges are generally considered as colonial organisms because there is little cell specialization and little separation of function/role. All cells do pretty much the same thing; it looks more like a pile of individual cells than an actual multicellular organism. In reality it is a little bit in between.

In any case, what one wants to call multicellular or unicellular is a matter of definition and preferences. You cannot find the line between unicellular and multicellular because there is no such line that would not be very arbitrary and filled with special cases.

You can study a little more the physiology of sponges and then decide for yourself if it looks sufficiently like a multicellular organism or more like a colony of cells (a colonial organism).

A collection of cells can maintain their individuality, and  have almost nothing in common but their location. No doubt all multicellular organisms today are descended from such collections.
To start doing anything useful for survival, the cells of such a collection can begin to specialize: some for locomotion, some for digestion, some for protection, and so on. Specialized cells group into tissues, and then into organs.
Organisms with cells responsive to electrical stimuli, which occur only in the animalia, can develop specialized tissue for movement, leading to muscles. They can also develop sensory organs, because excitable tissue gives them a mechanism for transmitting signals, and acting in response to sensory inputs.
A collection of cells without any of these specializations may develop into a syncytium, a mass in which there are  many cells sharing a common cytoplasm, with many individual cell nuclei lying in it. This arrangement allows them to share nutrients without having any specialized tissues or organs for doing so. Although there are multiple nuclei, it can almost be said that they live in a single, very large cell. Not having specialized tissues, they don't display the characteristics of multicellular organisms, and not having excitable tissue, they don't develop nervous systems.

This is the strategy some sponges have adopted, and that's why such sponges are not regarded as multicellular organisms.
Not all sponges are quite as simple as this, and have some differentiation in cell function. Whether these form tissues or not is a matter of definition.
So some sponges are almost entirely syncytial, and can't be regarded as multicellular, although they are metazoan. Some are a little more complex. And that explains why sponges will sometimes be regarded as multicellular, sometimes not. I guess it depends on the sponge.


Moth that resembles a leaf. What species is this? Location: Urban area near the Western Ghats, Kerala, South India

Date: Sometime in September, 2016

Climatic Conditions: Humid, frequent rains.

Brief description:

Head isn't prominent from the dorsal view. Wings outstretched even when at rest. Antennae largely concealed under the fore wings. Also it...um...does a pretty good impression of a leaf.

It resembles Pelagodes antiquadraria, which belongs to the moth genus Pelagodes in the family Geometridae.

Image Source: FlickRiver

Not a Moth, it's a Geometrid emerald butterfly.

http://www.fnanaturesearch.org/images/stories/ns/marked/M/7002.jpg


Why do the ancestors of birds still exist? If I am not mistaken, scientists believe that birds are evolved from reptiles. Why do the ancestors of birds (that is, reptiles) still exist?

Introduction to phylogeny
Short Intro to Speciation
Let's talk about speciation. Speciation is the process by which a single lineage split into two. This happens in a number of ways (allopatric vs sympatric vs parapatric, BDM model and others). I will consider a simple case of allopatric speciation below as it is the simplest one to understand (although not necessarily the process causing most speciation events).
Following the story of a lineage through its speciation events
Think of a population at time $t=0$. Let's call this species A (for Ancestor). Imagine that an ecological change brings a barrier right in the middle of the range of this population of A. Such a barrier could be originally caused by a fire, or a river that has changed direction or a mountain range "popping up". The two now isolated populations are free to diverge randomly through time. This is what we call a speciation event. Note that under this model, there is no necessary need for selection to explain speciation. Let's call the two diverging population B and C which exist at time $t=1$.
Now, imagine C goes under another speciation event and split into the populations D and E. In the same time, population B may have changed quite a bit so that we might want to call them F. Here is a diagram of the situation
  F           D ----- E     t=2
  |               |
  B ------------- C         t=1
          |
          A                 t=0

A is an ancestor of B,C,D,E and F and does not exist today. B is an ancestor of F but does not exist today. C is an ancestor to both D and E and does not exist today. Let some more time pass by and you may eventually end up with the following tree
  G ----- H       K   I ----- J t=3
      |           |       |
      F           D ----- E     t=2
      |               |
      B ------------- C         t=1
              |
              A                 t=0

At time $t=3$, only species G, H, I, K and J exist today, the other are ancestors of current species. Let's expand this tree even further.
  L ----- M   N       O       P ----- Q      t=4
      |       |       |           |
      G ----- H       K   I ----- J          t=3
          |           |       |
          F           D ----- E              t=2
          |               |
          B ------------- C                  t=1
                  |
                  A                          t=0

You will note that lineage I went extinct at some point between $t=3$ and $t=4$.
Naming subsets of the tree
Reptilia
I am now suggesting to give a generic name for all the lineages present in the tree we drew (which we call a phylogenetic tree by the way). Let's call them Reptilia. So all the species A,B,C,D,E,F,J,I,J,K,L,M,N,O,P and Q are Reptilia.
Birds and Mammals
Now let's consider a subset of this tree. Let's consider the subset made of the species J, P and Q only. Let's call them birds. Let's also call mammals the subset composed by the species G,L and M.
Lizards (and others)
Finally let's call lizards all reptilia that are not birds, nor mammals (in reality it would be more correct to call this group lizard_crocodile_turtles_snake_amphibians_tuatura). Of course, the right tree is much bigger! By the way, you can explore the tree of life yourself on OneZoom.org.
What is a taxon
By the way, a group of species is called a taxon (plur. taxa).
Monophyletic taxa
It might be straight forward to you that there is something fundamentally different between the groups that we called mammals, birds and reptilia to the one that we called lizards. Indeed mammals, birds and reptilia are called monophyletic as they are composed of a given ancestor and all its descendants. lizard on the other way is not monophyletic. A monophyletic taxon is also called a clade. Below is a graph representing what a monophyletic taxon is. It also uses the terms polyphyletic and paraphyletic to describe different types of non-monophyletic taxa

Concept of species
You might want to learn more about the issues behind the concept of species in the post How could humans have interbred with Neanderthals if we're a different species?
Concept of taxonomic ranks
What we decide to call a class, an order or a family is also somewhat arbitrary too. For example, we generally consider the monophyletic taxon Mammalia is a class. However, there is no non-arbitrary reason for calling Mammalia a class rather than Eutheria (eutheria = placental mammal).

Online resources
I suppose the above answered a big part of your question. You will be able to read all of what I just wrote (and much more) on any good introductory course to evolutionary biology. Consider having a quick look at Understanding Evolution by UC Berkeley for example as @MattDMo suggested in the comments.
Issues in your post
There are issues in your post that cannot be addressed in a single post (another reason for you to follow a quick intro course to evolution). Below I consider your post piece by piece mainly to point to some issues

Scientists believe

Terrible statement. By belief, we often refer to a non-justified belief, that is a belief about the world that is not justified (in science, the method of justification is called "the scientific method"). The statement, therefore, suggests that non-justified beliefs have a place in science while they don't. By being a little lose on the semantic, one could say that scientists "know" or they don't know but they don't believe without good reasons to believe.

that birds are evolved from reptiles

This is misleading (and it mislead you) because by "reptile" you think of a lineage that currently exists. Also, the expression "are evolved from" sounds very wrong. The expression "has evolved from" would be more correct.

evolution occur so that the organism can survive in the environment by developing new characters

This is wrong both in terms of the semantic (issue of causality when saying so that) and in term of the definition of evolution. You seem to confound evolution with natural selection.

According to natural selection

Natural selection is a process, not an explanation. It is like saying "according to gravity". The semantic is wrong, you should say "according to the theory of gravity" or "according to the theory of evolution" (or eventually "according to the theory of natural selection").

According to natural selection, those with favourable variations will survive and those with unfavourable die

You seem to apply that statement to population-level fitness (which would be mainly wrong) rather than to fitness variance within a population.

Why do the ancestors of birds (that is, reptiles) still exist?

The ancestors of birds don't exist anymore. I hope that was made clear from the above explanations.

Why didn't they get eliminated by natural selection?

This sentence suggests that you do not really understand what natural selection is but this is a story for another time. You can learn about natural selection on Understanding Evolution by UC Berkeley.

Reptiles evolving from birds is an example of divergent evolution. This wiki article has more information. Essentially both birds and reptiles are still around because they both fill a niche. That is, birds and reptiles separated have a common ancestor, and at some point their evolution diverged. At that point, birdoids which better filled the "bird" niche had higher fitness, and reptiloids which better filled the "reptile" niche had higher fitness, so birds evolved to be more like birds, and reptiles evolved to stay reptiles.


Can children restore brain cells? By "children" I mean young people at the age of 10 or lower.

I know that the adult brain cannot restore brain cells, but what about children? I mean, the brain must develop from a few cells to a 90 billion cells somehow, when do we lose this ability?

I'm also interested in cases when a child gets hit into the head (concussion). Can the damage  be fixed over time?

I am not an expert in neurobiology, but this is what I have been able to find:

In general, the PNS (peripheral nervous system) does have remarkable neuroregeneration capabilities. However, the CNS (central nervous system), which includes the brain, has extremely limited neuroregeneration abilities. However, there are some interesting examples of CNS recovery:

  Children under six who undergo, unfortunately, a hemiectomy, whereby one half of their brain is taken out, are able to regain almost normal function because of the brain’s ability to rewire and literally take over the functions of the missing other half of the brain.

I am guessing one thing that can explain this is that in children, the CNS is still developing, and so if there is damage, the CNS can just entirely replace damaged parts (this might be different than "fixing" which is required in adults).

Again, I am not an expert on this and would be glad to hear a neurobiologist's opinion.

This isn't quite the same; however, children can have parts of their brains removed and then the remaining parts of the brain can take over for that removed part. There are not also lasting effects of this even.

There is a neurosurgeon by the name of Benjamin Carson who has done a procedure called a hemispherectomy. A hemispherectomy is the act of removing one side of the person's brain. This procedure can only be done in children under the age of either 10 or 12 (I am so sorry, I can't remember right now).

The reason this can only be done in children is because the side of the brain not removed is able to take over for the removed side, this cannot occur in adults.


Why is polyploidy much more common in plants than in animals? There are very few animals with polyploidy like salamanders. Why is it that polyploidy is so uncommon in animals? On the other hand there are numerous examples of polyploid plants. If ut something to do with the gene dosage, how does it not affect plants?

Polyploidy is common in plants than in animals because in animals sex determination mechanism involves number and type sex chromosomes. Polyploidy will interfere with this mechanism and hence it is seen rarely in animals. I believe its probably because an animal progeny with multiple sex chromosomes won't be able to reproduce more of its kind unless it can also reproduce asexually (which is seen in plants as mentioned below).

Plants, on the other hand do not have any such sex determination (based on number or type of chromosomes) and majority of them can also reproduce vegetatively. This vegetative propagation enables multiplication of polyploid plants. Sexual reproduction will result in loss of desired polyploidy as per the principle of segregation. However, if a polyploid plant can produce a viable progeny sexually, it might have a different ploidy than its polyploid parent which won't happen if the parent reproduces asexually. Hence, polyploid plants can be classified as sterile and fertile polyploids (the reference will give a detailed account on this mechanism).

Refer the section of Polyploidy (page 115, Chapter 6) of this book (Principles of Genetics, Snustad and Simons, 6th edition)

When it comes to gene dosage, animals do show gene compensation of X-linked genes by various methods. Example- formation of Barr Body in human females (Note that this has nothing to do with polyploidy, but happens since females have one X chromosome more than males). Whereas gene dosage in polyploid palnts has been exploited for improved agricultural yields as they have shown better productivity than their diploid couterparts.


What are the distinct neurochemical components of sexual pleasure? Sexual activity is usually described as pleasurable.

What neurochemical systems does sex activate? Does the presence or absence of a partner make a difference -- say, in the activation of the oxytocin system?

Undoubtedly, sexual activity is salient, and so it surely involves dopamine. (Salient activities, whether painful or pleasurable, activate the dopaminergic system.)

What about these systems:

adrenergic
gabaergic
cannabinoid
nicotinic
opioid
serotonergic
cholinergic
glycinergic
histaminergic
glutaminergic

Sexual response is primarily related to nitric oxide and its products. All of the systems you mentioned play a role, however the core pathway is from touch stimuli, to oxytocin release, to nitric oxide and dopamine accumulation, to motor response (orgasm) followed by prolactin to counteract said neurochemicals and temporarily suppress sexual response.

Sex gives you dopamine, oxytocin, adrenaline, and endorphins.


What is the difference between SOLiD, 454, and Illumina next-gen sequencing? I've started teaching myself about next-generation sequencing in preparation for a new job, and I'm wondering what the main differences are between the 454, SOLiD, and Illumina/Solexa machines, in terms of sample/library preparation and chemistry. How difficult is it for a protein veteran but next-gen newbie to get high-quality useful reads? I'm mainly going to be looking at antibody diversity, but consider this in general terms for any next-gen project.

I understand the basic theory of fluorescent chain-termination sequencing, but it's been a number of years since I last did it, and my career is now taking me back into the DNA realm.

Here is a short summary of the sequencing technologies you listed. Illumina is the most frequently used one.

Roche/454 FLX Pyrosequencer technology is based on pyrosequencing method, which utilizes the use of the enzymes ATP sulfurylase and luciferase. After the incorporation of each nucleotide by DNA polymerase, a pyrophosphate is released, which further takes part in downstream light-producing reactions. The amount of light is proportional to the incorporated number of nucleotides. The DNA is fragmented and adapters are ligated at both ends. The fragments are mixed with agarose beads, which carry adapters complementary to the library adapters, and thus each bead is associated with a unique DNA fragment. The beads and DNA fragments are isolated in individual micelles, where emulsion PCR takes place and million copies of the single fragments are amplified  onto the surface of each bead. Each bead is placed in a well of picotiter plate (PTP), as the wells have dimensions such that only one bead can fit per well. Enzymes are added to the beads and pure nucleotide solutions are added with an immediate imaging step. On one side of the array a CCD (charge-optic device) camera records the light emitted from each bead. The first four nucleotides (TCGA) are the same as the start of the adapter, which allows for the emitted light to be calibrated according to the type of nucleotide added. The major disadvantage of this method is the misinterpretation of homopolymers (consecutive nucleotides, e.g. AAA or CCC). Such areas are prone to insertions or deletions, as the length of the stretch can be inferred only by the intensity of the light emitted. On the other hand, substitution errors are very unlikely. The 454 FLX instrument generates ~400 000 reads per instrument-run, as the reads are 200-400bp. The greatest advantage of this platform is the read length, which is the longest of all second generation technologies. Although sequencing on 454 platform is more expensive than sequencing on Illumina platform (40USD per Mega base versus 2USD per Mega base), it could still be the best choice for de novo assembly or metagenomics applications. (Mardis, E., 2008, Shendure, J. and Ji, H., 2008).

Illumina is the most frequently used one. The DNA to be sequenced is fragmented into about 200 base strands. Adapters are ligated onto the ends of the fragments and one of these adapters is hybridized on a flow cell. Illumina essentially utilizes a unique "bridged" amplification reaction that occurs on the surface of the flow cell. Localized PCR reaction is performed, and each of the hybridized pieces of DNA will get locally amplified to generate clusters which will have the exact same molecule. Subsequently, the DNA sequence is determined by adding a primer on one of the ends of the molecule. A mixture of modified nucleotides is added. Each one of them carries a base-specific fluorescent label attached to it. Also, each one has the 3' OH group blocked which ensures the incorporation of one nucleotide at a time.  The flow cell is placed under a microscope and when light is shined on its fluorescence, the emission light shows which base was incorporated on each one of those clusters. The Illumina read length is approximately 35 bases, but over billion reads are generated at a time. The major error type is substitution, rather than deletion or insertion (Mardis, E., 2008, Shendure, J. and Ji, H., 2008).

The SOLiD platform utilizes the use of DNA fragmented library, which is flanked by ligated adapters. The fragments are attached to small paramagnetic beads and emulsion PCR is performed to amplify the fragments. In contrast to the other sequencing platforms, sequencing by synthesis is performed by utilizing DNA ligase, rather than polymerase. Each cycle of sequencing involves the ligation of a degenerate population of fluorescently labeled universal octamer primers. A specific position of the octamer (e.g., base 5) carries a fluorescent label. After ligation, images are acquired in four channels, followed by cleavage of the octamer between positions 5 and 6, removing the fluorescent label. After several rounds of octamer ligation, which enable sequencing of every 5th base (e.g., bases 5, 10, 15, and 20), the extended primer is denatured. Different primers can be used to examine the previous or next positions (e.g., base 3 or 6).  The platform can use primers which carry two adjacent correlated with label bases. This approach involves the examination of the bases twice in a cycle, which decreases the error rates. SOLiD read lengths are 25-35 bp, and each sequencing run yields 2–4 Gb of DNA sequence data (Mardis, E., 2008, Shendure, J. and Ji, H., 2008).

References:

Mardis, E., Next generation DNA sequencing methods. Ann. Rev. Genomics Hum. Genet, 9: 387-402 (2008). DOI 10.1146/annurev.genom.9.081307.164359
Shendure, J. and Ji, H., Next-generation DNA sequencing. Nat. Biotechnol., 26: 1135-1145 (2008). DOI 10.1038/nbt1486

It's not easy to write down a comprehensive answer to your question, I would suggest you read this paper Field guide to next-generation DNA sequencers, which provide very good comparison of the NGS platforms


What type of bee/wasp is this? I found some bees or wasps, in my garden.

Auckland, New Zealand
13mm long head to abdomen, fluffy on thorax and head. Abdomen is orange brown with black stripes.

The nest or hive is underground (otherwise I'd suspect honey bee, though they seem a little smaller even than honey bee workers).

I managed to catch one eventually, but then I realised the container had oxide powder, so the bee in the attached picture is a lot blacker than it was in life. It is also dead ( just in case that's not obvious)

They don't seem to be aggressive - there is a new fence being built right past their nest, they don't seem to be bothered by it.

I am a beekeeper but only beginning, so I do have honeybee workers to compare it to, but not a whole lot of experience.

NOTE: it is autumn (fall) here - high temperature was 23° c (73° f)

It is a vespid wasp (family vespidae). Bees are generally hairy, and this one has the typical wing folding of a vespid. Genus Vespula. There is a New Zealand website that shows the differences among common NZ wasps here:
https://www.landcareresearch.co.nz/science/plants-animals-fungi/animals/invertebrates/invasive-invertebrates/wasps/identification/key-differences

Looks like it might be a European tube wasp


What is meant in biology by the term "evolved"? A student asked me this the other day and I thought that I would ask it again here. If one organism is said to be "more evolved" than another, what exactly does this mean?

"More evolved" is actually meaningless in all contexts. See terdon's answer for a good explanation.

In the strictest sense, an organism can be said to be more divergent than another when comparing both to an outgroup, such that there is an inferred most common ancestor in reference to which to make the comparison. In this case, one organism is more divergent if there are more changes to this organism than the other, relative to the reference point.

However, when speaking, many people get lazy, and use "more evolved" as shorthand, wishing it to mean something like "more divergent". Even "more divergent" is meaningless in the following contexts:

when there is no outgroup understood
when describing increasing complexity (obligate parasites have lost complexity and have had more evolutionary changes than their non-parasitic relatives)
when the outgroup is poorly chosen. Mammal vs reptile comparisons should not, in general, use prokaryotes as the outgroup.

Edited 2013/12/06 to reflect the precision in the answer by terdon.

I have mostly seen it used to mean "possessing features that appeared most recently in the historical evolutionary record". Thus a human is considered more evolved than a chimp because our bipedality, hairlessness and large brain appeared more recently than the features of chimps, and a chimp is more evolved than a fish because fish very similar to ones alive today appear in the record before anything resembling an ape, and so on.

I think it's pretty poor use of language, frankly, since it suggests linearity and ordering to evolution that is simply not there, conflates gross morphological change with change in general and incorrectly implies that stabilising selection is not evolution.


Why did viruses evolve in the first place? This question might seem kind of strange, but it's something I've been chewing on for ages, and I can't really think of a good answer.

Viruses just seem to be floating around passively until they encounter a host cell. Then they enter the host cell, wreak havoc and use the host cell machinery to make more copies of themselves. Then these copies float around passively, until they find host cells.

So what's the point of all this? Infecting the host and causing so much trouble for the host, I mean. The only thing I could think of was something like the "selfish gene" hypothesis, i.e. the genetic material of the virus wants to make as many copies of itself as possible, and in order to secure the machinery for replication, it must infect a host cell. But it's not a very satisfying answer, somehow. All other living organisms at least have their own replication machinery. Then what kind of organisms are viruses? (Are they even organisms?) How and why did they evolve and stay around on the earth for so much time (till the present), if they depend on hosts for their replication?

The are different theories about virus evolution, some speculate that they were evolved before the cells, some speculate they are evolved to spread genetic information, a sort of specialized conjugative pilus others say that they are cellular parasites. Still, none has the final answer yet, but thanks to the boost of DNA sequencing, many new pieces of the puzzle come out lately so keep updating your knowledge!

Whether they are alive or not is also matter of discussion and it pretty much depends on the definition of life itself.
If you define life as the property of reproducing, transmitting genetic information and evolve, then viruses are life forms. But if you want to include in the definition that a life form must have all the biomolecular machinery encoded in the DNA (I really disagree on this point), then they are not. To me, they look quite a living thing.

About your sentence:

  So what's the point of all this? Infecting the host and causing so
  much trouble for the host...

I think you are looking only at the "negative" side. Viruses can transfer useful genetic information, plus they are involved with the evolution itself. We humans have lot's of viral DNA in our genome, so no viruses, no humans as we know them. Think about it ;)

There are plenty of resources around to get a better insight please have look at the following links to get started.

https://en.wikipedia.org/wiki/Viral_evolution

https://en.wikipedia.org/wiki/Evolution_of_influenza

http://www.sciencedirect.com/science/article/pii/S0042682215000859

https://link.springer.com/article/10.1007/s00239-013-9601-0

https://www.nature.com/search?order=relevance&q=evolution%20of%20viruses

Viruses actually have RNA. Due to this property of genetic material, RNA organisms are faster than DNA organisms!
Secondly, they have a protein coat that acts as another important thing which makes allows them to live in contact with organisms!
But every coin has two sides. It is much used in biotechnology to transfer important genes in plants and animals by disarming their pathogenic properties!
When they come in contact with host DNA, host DNA starts to replicate its virus genetic material and then its own! For example, in the case of HIV.

See in the image how reverse transcription the most important process converts RNA -> DNA then creates an infected DNA strand in host and host produces its RNA which is infected!


Deliberately choosing one nostril to breath through James Nestor, on pp. 41-42 of his book Breath: the New Science of a Lost Art, claims the following.

The right nostril is a gas pedal. When you're inhaling primarily through this channel, circulation speeds up, your body gets hotter, and cortisol levels, blood pressue, and heart rate all increase. This happens because breathing through the right side of the nose activates the sympathetic nervous system, the "fight or flight" mechanism that puts the body in a more elevated state of alertness and readiness. Breathing through the right nostril will also feed more blood to the opposite hemisphere of the brain, specificially to the prefrontal cortex, which has been associated with logical decisions, language, and computing.

Inhaling through the left nostril has the opposite effect: it works as a kind of brake system to the right nostril's accelerator. The left nostril is more deeply connected to the parasympathetic nervous system, the rest-and-relax side that lowers temperature and blood pressue, cools the body, and reduces anxiety.

... Our bodies operate most efficiently in a state of balance, pivoting between action and relaxation, daydreaming and reasoned thought. This balance is influenced by the nasal cycle, and may even be controlled by it. It's a balance that can also be gamed.

A question on this site describes we only breathe out of one nostril at a time: at any given time, one of our nasal cavities will be more open than the other, and this switches back and forth every couple hours. For the most part, we are unaware of this. (At any rate, I was!)
I am very curious about Nestor's claim that the balance can be gamed. It seems that one could prepare effectively for a math exam by practicing right-nostril breathing, or for sleep by practicing left-nostril breathing. Is this the case?

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3681046/
Assessment of the Effects of Pranayama/Alternate Nostril Breathing on the Parasympathetic Nervous System in Young Adults
Result and Conclusion: This study showed that the parasympathetic tone was enhanced appreciably in the participants. The observations of this study suggest that the yogic exercise of A.N.B. influences the parasympathetic nervous system significantly.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3978938/
Slow Yogic Breathing Through Right and Left Nostril Influences Sympathovagal Balance, Heart Rate Variability, and Cardiovascular Risks in Young Adults
Short-term practice of LNB improves vagal tone, increases HRV, and promotes cardiovascular health of medical students. Practice of RNB increases sympathetic tone and could jeopardize cardiovascular health.

There seems to be some evidence that this works.


Why do some mammals not have testes in a scrotum? Coming from an evolutionary approach, Is the only purpose of a scrotum to regulate the temperature of the testes?

Knowing all mammals are warm blooded, shouldn't all mammals have testes in a scrotum?

Having descended testes is a derived characteristic within mammals; monotremes and the Afrotheria (including elephants) all retain the ancestral character state (Kleisner, et al., 2010)2. Among those mammals with descended testes, these can be ascrotal or scrotal. Testicular descent is hypothesized to have only occurred once within Mammalia, with the ascrotal Laurasiatheria. Descended ascrotal testes are found in cetaceans, phocid seals, hippos, tapirs, rhinos, and some bats. Descended scrotal testes are found in horses, pigs, camels, and Carnivora.

Since basal mammals would presumably have to regulate testicular temperature just as much as derived mammals, the temperature regulation hypothesis seems to not hold up. So the real question is: why have a scrotum? One hypothesis has to do with evolution of fast locomotion (e.g., galloping).

According to Frey (1991, 40)4:

  The strong flexions and extensions of the vertebral column during
  gallop should cause intense fluctuations of intra-abdominal pressure.
  Fluctuations of intra-abdominal pressure severely impede continuous
  flow of blood in the abdominal veins. Periodically reduced venous
  drainage resulting in fluctuations of intra-testicular pressure would
  impair the process of spermiohistogenesis, which is dependent on an
  absolutely constant pressure within the testis.

Chance (1996)5 suggests that the temperature hypothesis might represent a secondary adaptation:

  Because in the human male, scrotal testes function optimally at
  temperatures below that of the body, much speculation, and a
  considerable amount of research, has gone into attempting to see what
  (metabolic) advantage might accrue from this lower temperature,
  without considering the possibility that this is a secondary
  adaptation to an enforced external position.

Kleisner, K., Ivell, R., and Flegr, J. 2010. The evolutionary history of testicular externalization and the origin of the scrotum. J Biosci 35:27-37

Frey, R. 1991. Zur Ursache des Hodenabstiegs (Descensus testiculorum) bei Säugetieren. Z Zool Sys Evolut-Forsch 29:40–65

Chance, M.R.A. 1996. Reason for externalization of the testis of mammals. J Zool 239:691–695

Elephants do not have a scrotal sac. One of the reasons may be their basal metabolsm is very low. Hence chance of an increase in body temperature is meager.Animals with higher metabolic rate will have scrotal sac.


How does new species come into existence? The only reason for the creation of new species that I found from the internet is geographical isolation. Are there any more reasons?

A paper from Müller et al. proposes a molecular marker called a CBC, differences in which can be used to call two different species, even when closely related: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1950759/

  In this study we are looking for a molecular classifier that might indicate that two organisms belong to different species. We are interested in an indicator hypothesis that is easy to work upon and additionally yields a certain probability that two organisms belong to distinct species. Compensatory base changes (CBCs) in the internal transcribed spacer 2 region (ITS2) of the nuclear rRNA cistron have been suggested as such a classifier.

Some mutation event that creates sufficiently different CBCs in a viable offspring capable of further reproduction, i.e., survives natural selection, would therefore lead to speciation, by this measure.


How do nerve impulses travel so quickly? Nerve impulses must travel incredibly fast to achieve the functions they do. However, I have been taught that sodium ions move down the axons by diffusion (thus causing depolarisation of the next part of the membrane etc, and this is the action potential).

However, I was under the impression that diffusion is a very slow process? How can this be the case?

There is a large gradient created by selective permeability of Na channels and as you're probably aware the speed of diffusion is proportional to the electrochemical gradient.

Very small numbers of ions actually cross the membrane during depolarisation and subsequent AP events.


Why do most organisms have negative supercoiled DNA? It has been observed that in nature most organisms have negative supercoiled DNA and that few organisms have positive supercoiled DNA. Some of the organisms that have the positive supercoiled DNA live in strong acidic environments but are very rare compared to negative supercoiled DNA. Why wouldn't all organisms have the same DNA supercoiling? Does it affect their survival in any way?

One important notion in DNA topology is the linking number ($Lk$) which is the sum of right-handed twisting # and left-handed writhing # ($Tw+Wr$). Say the $Lk = x$ for relaxed DNA. If $Lk<x$ then you have negative supercoiling while positive supercoiling happens when $Lk>x$.

The higher the $Lk$ value the higher the helical energy of the DNA and the harder it is to separate it meaning the DNA is now more stable. In so-called "extreme" conditions (e.g. high acidity or high T˚) the organism must protect his DNA from degradation. Therefore those organisms require a more stable form of their DNA which can be achieve by positive-supercoiling and/or high GC content.

Now why do the vast majority of the organisms have negatively-supercoiled DNAs? If you let the DNA by itself, it will adopt an $Lk=x$, i.e. it will be in his "relaxed"-form. Negative supercoiling arose because of the presence of Topoisomerases (type I and II), which are proteins that cleave the DNA and release the helical tensions and which cumulatively provokes the DNA to be slightly underwinded compared to it's relax-form. Is this good for the organism, if living in non aggressive conditions? Yes it is because a decrease of the $Lk$ will make the DNA easier to separate. This means replication and transcription can occur more easily or in proper terms, they now require less energy to perform their functions.

Here an excellent reference on this subject as well as a Youtube video that explains those concepts using strings. The latter is really helpful as those concepts are easier to understand visually than in writing.

I hope this helps.

in negative super coiling  number of the times the strands cross each other is LESS than positive super coiling making it easier to unwind it for the processes of replication,transcription....


Aquatic Snail Identification I can’t for the life of me find an identification of these snails. They’re thriving in brackish water, but may be freshwater naturally. They’re about .8cm long at their largest. I believe they have live birth due to the lack of eggs but presence of baby snails over the year and a half that I’ve had them.

Looks like a Malayan Live Bearing snail , fairly common in the US aquarium trade. I have inadvertently gotten them into all my tanks. Common aquarium fish can't eat them ( unless you crush them on the glass). I did not know they can tolerate brackish water. Yhey will get to 1.5 mm.


What is this grainy surface on my two-week-old sourdough starter? I'm baking bread at home as a hobby, using sourdough. After skipping one baking day, I haven't used my sourdough starter for two weeks. When opening the jar in which I keep it, I saw the surface had taken on this unusual look. When viewed from the side through the glass, the contents looked normal below the surface.

The sourdough starter consists of whole rye flour at 100% hydration (flour:water = 1:1). I had removed it from the ripe sourdough on the last baking day and have since kept it in the refrigerator with a lid (only loosely screwed on) for 13 days.

Normally I'm using it already after keeping it for 7 days, and I'm used to the surface turning light gray and dry (but smooth and soft) after that time, which didn't ever seem to be a problem. Now the color of the surface was identical, but it has become grainy, like tiny worms.

I have removed and discarded the top layer (3 mm). It was soft (unlike dried out, crusty, dough) and smelled a bit like fresh yeast. Below that, the contents smelled normal, like very ripe sourdough.

The jar is about 6 cm in diameter and was filled to about 2 cm (→ volume of the starter ≈ 60 ml).

What are we looking at here? Could it be actual yeast cells (or other microorganisms normally found in sourdough)?
Is it harmful?

After 13 days (click for full-resolution version)

Reference pictures

After only 2 days, the starter looks like this:

(click for full-resolution versions)

Naturally, when you create dough you expect it to rise in size the following few days. That's just a chemical reaction that allows air to enter the dough body and traps it in tiny bubbles. My theory is that if the dough is not as high as expected that the air has escaped it because of the extra time you left it.

The pattern is not unusual and is the result of the deflation I'm talking about.

It's probably still safe to eat, but the bread won't be as good(eat at your own risk)


Sheep vs. Furry animals Why can't we take the fur of a fox without killing or skinning it just like the sheep , what's the biological or chemical structure or even the trait which is on a sheep's body that separates wool from its skin
Why can't we apply the bioclip technology on furry animals too ?

Fur, wool, and hair are all made of keratins.

To the best of my knowledge wool and fur are separated arbitrarily, based on the properties of the fibres. This arbitrary division allows rabbits to have fur but selective breeding has produced angora rabbits, which have wool. The opposite should be possible, with time you could breed a sheep that has fur.

Length; Wool grows continuously and animals are clipped when the fibres are long. Fur often has a maximum length.

Structure: The structure of the keratin in the wool makes the fibres kinked (crimped). These kinks aid the production of fabrics. I believe the cuticular scales also aid in the production of fabrics.

Fur doesn't have kinks, so even if it's long enough to weave the fabric is likely to lack durability.

Some furs are used in textiles rather than pelts. Possum fur is 'plucked' and woven into fabrics with wool. The resulting fabric is slightly less durable. However, possum fur is hollow and smooth so possum fur fabrics are very soft and warm. The clothing is very good to to wear.

However, fur is generally inferior to wool for textiles and it took a couple of decades to develop techniques to produce textiles from possum fur. This happened because of odd ecological and economic drivers. Possums are are a major pest species in New Zealand where they contribute to the decline of native birds and insects. Millions of possums are killed every year in New Zealand. The market for possum skins is very small. This is why so much effort was put into producing a fabric from possum fur.

So you could shear a fox and produce a fabric but the fabric would likely be poor and there's no reason to do so.

Sheep wool is like cutting long curly human hairs: they stick together due to the length and curliness.

For foxes, chita, rabbit, lions, etc, the hair are really short and parallel: it's like cutting your eyebrows: they won't stick together. That why you (used to) find them as carpet, kept with the skin.


Why Only DNA can Contain Hereditary Material? Well I'm well aware that it is proven that DNA contains  genetic material via transformation and Hershey-Chase Experiment of T2 bacteriophage. Still I was wondering what is the reason only DNA contains it and not protein or RNA.
What I've learned is that DNA is the most stable of all these molecules and it has the ability to replicate itself.
Other than this I can't find any solid answere.
Thanks!

I think any discussion of this question can benefit from a historical perspective. For a long time, it was in fact believed that proteins was the hereditary material. The Nature Scitable page on the discovery of DNA (1) starts with the following passage:

  In the first half of the twentieth century, Gregor Mendel's principles
  of genetic inheritance became widely accepted, but the chemical nature
  of the hereditary material remained unknown. Scientists did know that
  genes were located on chromosomes and that chromosomes consisted of
  DNA and proteins. At the time, however, proteins seemed to be a better
  choice for the genetic material, because chemical analyses had shown
  that proteins are more varied than DNA in their chemical composition,
  as well as in their physical properties.

While perhaps easy to dismiss in hindsight, it is possible to understand the reasoning of the day. The "central dogma" of molecular biology, that genetic information flows from DNA to RNA to proteins was only described later, and explained how the production of complex proteins consisting of 20-odd amino acids can be directed by a polymer consisting of only four nucleotides. This allows great complexity and variety in phenotypes while maintaining simplicity of the genetic material. The central dogma also facilitates the seperation of the use (through protein expression) and storage (as DNA) of genetic material.

As Watson and Crick noted in their famous paper, the double helix of DNA, when discovered, immediately suggested how the genetic material could be elegantly copied. While the more complex structure of proteins would likely require a more complex copying mechanism, the specification of amino acids through three-nucleotide codons in DNA allows the regularity of the DNA material to be retained for easy replication while allowing complex proteins to be produced.

However, even though DNA is the primary genetic material today, the situation may have been different at the time life first appeared. According to the RNA world hypothesis, RNA may have been the original genetic material and that DNA is a variation of RNA, not the other way around as it is commonly seen.

For a fuller historical perspective, I recommend the book "What is Life?" by Erwin Schrödinger, which was written before the discovery of DNA as the genetic material.

The simplest answer one could offer to this question is hidden in the structure of the DNA itself. DNA is double helix structure with the presence of 3'->5' end and 5'-3'  coiled helically in the double strand ( it is the direction in which DNA is synthesised as per formation of replication fork via the enzyme DNA dependent DNA polymerase.

The inability of the Proteins, amino acids etc to replicate themselves makes no sense to have them as genetic material ( as also concluded by Martha and chase experiment).
Now, here is the point which leads the most logical question?
Why not RNA ?
In fact it is much better in the Job that DNA does, it is very fast in replication almost have the same structure,  but the fact that the presence of OH group makes RNA very reactive and Unstable does not make it idle for transfer of hereditary material in nature, we should know that thousands of nucleotides are synthesized by DNA polymerase during the replication of DNA from the template DNA which is highly accurate and precise even slightest of error can lead to very big mutation and the presence of the Deoxyribose and complementarity principle makes the DNA best suited for Genetic material.

Although a whole of a different class of the organism exists that have RNA as genetic material, they are called retroviruses eg. HIV virus so the question that DNA is the only genetic material in all living organism is not true, although yes it is the genetic material in Humans and majority of the organism due to the above reasons.

EDIT : AS @WYSIWYG mentioned there are also many viruses which have RNA as genetic material but are not called Retroviruses, nonetheless DNA is not the only genetic material that exists.

Kapeesh !


What is the evolutionary advantage with two lungs (kidneys)? What is the evolutionary advantage with two lungs (kidneys)? Most living beings only have one heart, one stomach. Most internal organs are not doubled and if one lung fails it is not exactly quite transparent due to having an extra lung. Before modern health care one failed lung would kill the individual.
The same can probably be said for kidneys.

Humans and most organisms have bilateral symmetry.  Anything that is on the left side of the body will be on the right also.  Not everything can be in the middle, so ... you end up with two.  This is evolutionarily labile - for example, fish generally have one dorsal swim bladder, though it is derived from the lungs.  In a similar manner, the heart is formed by the fusion of primordia on either side during development - see UNSW for a cute video.

Eels have two lungs and so do lungfish and all vertebrates, so the design is at least 375 million years old, although vertebrate lungs have developed different air flow systems, i.e. birds and iguanas. No vertebrates have a very small and big lung as far as I know.

Rib punctures can affect one lung which fills with fluid.
Stick and tooth punctures can actually cause air to escape the lung through the chest, a condition that can sometimes be survived in th wild, but less likely with only one lung.
Pulmonary infections can cause a lung to fill with water, so having two lungs gives some extra protection.
Breathed in objects like twigs can sit inside a lung for many years and cause weakness, for example a man coughed up a twig from his lung 14 years after having breathed it in while playing in a hedge with friends.
Two lungs may also bring higher surface area and higher performance than one lung.


Why does photosynthesis occur even in blue light when the photocentres are activated in red light From Engelmann's experiment

  Engelmann used this device to illuminate a strand of Cladophora (not Spirogyra) with light from the visible spectrum, exposing different sections to different wavelengths (or colors of light). He added the oxygen seeking bacteria B. termo to this setup and noted where they accumulated (Note: Four years later, Hauser concluded that B. termo had been mislabeled and was not one, but three species of bacteria of the genus Proteus [2]). Their clumping allowed him to see which regions had the highest concentration of oxygen. He concluded that the most photosynthetically active regions will have the highest concentrations of bacteria. The bacteria accumulated in the regions of red and violet light, showing that these wavelengths of light generated the most photosynthetic activity.

It can be concluded that the photosynthetically active regions of light are present at the blue-violet region and the red region

What I am unable to understand is , if photosystems I and II are activated at light wavelengths of 680nm and 700nm (primarily at the red region of the spectrum) then what type of photosynthesis is happening at the blue region due to which there is oxygen evolution?

My attempt:

The antenna molecules (light harvesting complex) which absorb majorly at this wavelength are transferring energy to the photocentre due to which there is excitation of the photocentre and thus OEC gets activated.

Even if this were true, then should'nt blue light be as effective as red light in helping in generating the quantum yield?

While it is true that strongest activity of Photosystem I and II happens with 700nm and 680nm light, these are not the only wavelengths that can be used for photosynthesis.

The green color of plants comes from chlorophyll, which is the main light absorbing component in the photo systems. If chlorophyll had only a single absorption peak at 680-700nm, it would have a blue(-ish) color instead of a green one.

Looking at the absorption spectrum of chlorophyll (which wavelengths it can absorb how well), you can see that there is a a second peak around 400nm:

This both explains the results of Engelmann's experiment and the green color of chlorophyll (with both red and blue colors removed only green remains)

Picture taken from: http://hyperphysics.phy-astr.gsu.edu/hbase/Biology/ligabs.html

The answer you are looking for is most certainly here:

https://en.wikipedia.org/wiki/Cryptochrome


Calcium for Humans: Supplements vs Fortified Sources I'm trying to be vegan, and purely natural foods lack sufficient calcium for the Recommended Daily Intake. Links 2 to 4 (but not 1) assert a correlation between calcium supplements and disease.

  [1. WebMD :] "Keep in mind that there's really not that much difference between getting calcium in a supplement and calcium in food."
  "Calcium-fortified foods -- such as cereals, some juices, and soy milk -- are excellent sources of the mineral, experts tell WebMD."

  [2. health.harvard.edu :] An 8-ounce portion of off-the-shelf orange juice contains about 300 mg of calcium. The calcium in fortified soy milk also compares favorably to whole milk.
  Breakfast cereals (which are also fortified) contain substantial amounts of calcium, especially when combined with low-fat milk.
  A portion of oatmeal on its own contains just 100 mg of calcium. “But if you cut up some dried figs and add it to a bowl of oatmeal with milk, you easily get about half of what you need without having any supplements,” Dr. Hauser says.

  [3. NY Times Blog :] All the researchers agree that, given the widespread use of supplemental calcium, better studies are needed to clarify possible risks and benefits, and to whom they may apply.

  Until such information is available, consumers seeking to preserve their bones would be wise to rely primarily on dietary sources of the mineral and to pursue regular weight-bearing or strength-building exercises, or both. Walking, running, weight lifting and working out on resistance machines is unquestionably effective and safe for most adults, if done properly.

  [4. NY Times :]  The institute’s expert committee, which included bone specialists, concluded that most people don’t need supplements of these critical nutrients and warned of serious health risks from the high doses some now take — including kidney stones and heart disease linked to calcium supplements, and the very falls and fractures that vitamin D is meant to protect against.

5. How and why would the calcium carbonate from calcium supplements be asserted as worse than that in the fortified foods?

6. Isn't solid calcium carbonate (e.g. in supplements) chemically the same as aqueous calcium carbonate (e.g. in fortified drinks)?

7. Are calcium supplements really worse than fortified foods with calcium?

This is close to a personal medical question, so I'll try and be vague and avoid advice.

There's nothing inherently bad about calcium supplements, and those links and thousands of others that are easy to find tend to all say that same thing.  Basically, for typical people on a typical diet, enough calcium is supplied through food that supplements are unnecessary.  The problem arises when people take too many supplements, such that their intake is significantly higher than the daily recommended intake.  These people can experience a number of symptoms, including kidney and heart failure.  Fortified food and supplements are, as best as I can tell, no different, except that food is simpler route for intake with built-in limit-setting.  That is, you can easily pop five calcium pills (BAD IDEA) but nobody is ever going to drink five containers of fortified soy "milk" on a whim.

My go-to example is that of astronauts.  Astronauts who are in space for extended periods of time must take calcium supplements, in addition to a strict exercise regimen to help stem the tide of bone loss.  Bone loss still occurs, however, because they can only take so much calcium before it starts to cause serious heart problems.  There's nothing inherently wrong with calcium supplements but for most people they are completely unnecessary.  You should talk to your primary care physician and perhaps a dietician.

1 - probably because of regulation in the U.S. (and maybe other nations??). Nutrients added via fortification are regulated by the F.D.A essentially as foods.  Nutrients in supplements are regulated essentially as manufactured goods.  The difference -- despite both being ingested by us -- is a major source of concern. See http://www.fda.gov/Food/DietarySupplements/

3 - as a patient, that question is best answered by your doctor via blood sampling. My doctor found VitD deficiency in me, which can cause calcium uptake problems; but like the previous answer, people who aren't monitoring their serum levels and medicating themselves could overdose on any fortified or supplement nutrients.


Help to identify larva found in sink? I need some help in identifying this critter. It was found in southeast Georgia in a home I am renovating. There were several around the sink and toilet bowl.

Approximately 5 millimeters long. Stripes black/dark gray. Tapered end seems to be moving as though it was the head. Bulbous end has two extrusions like antennae?

Thanks in advance.

Found it!

Seems to actually be the pupae phase of the common drain fly - psychoda spp.

Looks like I'm going to be routing or replacing the pipes in that house.

Thanks.


Major groups of photosynthetic prokaryotes According to Stryer there are four major groups of photosynthetic prokaryotes, i.e. Table 19.1

Bacteria Photosynthetic electron donor $\ce{O2}$ use.

Green sulfur $\ce{H2}$, $\ce{H2S}$, $\ce{S}$ Anoxygenic.

Green nonsulfur Variety of amino acids and organic acids Anoxygenic.

Purple sulfur $\ce{H2}$, $\ce{H2S}$, $\ce{S}$ Anoxygenic.

Purple nonsulfur Usually organic molecules Anoxygenic.

Cyanobacteria $\ce{H2O}$ Oxygenic.

Do each groups belong to a different genus?

To answer your question, yes they are all in a different genus, but that’s really specific.  If you are wondering about their fundamental differences, they fall into a few different groups.

Green sulfur bacteria usually falls into the phylum Chlorobi

Green non-sulfur bacteria falls into the phylum Chloroflexi (Part of the terrabacteria superphylum)

Cyanobacteria is a phylum in itself but also falls into the terrabacteria superphylum.

Both, Purple sulfur/non-sulfur bacteria are all proteobacteria.

Now, pay attention here, as linking these could be somewhat confusing sometimes.  But now we can link together their relationships.

Green sulfur bacteria (Chlorobi) falls into the FCB superphylum, meaning that it is a gracilicute.

Purple sulfur/non-sulfur bacteria (Proteobacteria) are also gracilicutes.

Green non-sulfur bacteria (Chloroflexi) is part of the terrabacteria superphylum.  Terrabacteria are not gracilicutes.

Cyanobacteria is also in the terrabacteria superphylum. (Again, not a gracilicute.)

Now that we know this, we can reasonably assume that both purple sulfur/non-sulfur bacteria are related to green sulfur bacteria, as they are both gracilicutes.  Also, we can conclude that the non-gracilicute green non-sulfur bacteria and Cyanobacteria are more closely related to each other than they are to the latter mentioned bacteria.

Here’s another cool fact, some Deinococcus-Thermus bacteria (members of the terrabacteria superphylum along with Cyanobacteria and Chloroflexi) have been found to carry the bacteriophytochrome photoreceptor (BphP) which absorbs red light.  Interestingly, Deinococcus-Thermus are non-photosynthetic, but these photoreceptors are found in photosynthetic Chloroflexi as well. This indicates that the deinococcus bacteria likely diverged from chloroflexi at some point but still retained the BphP.

Hope this helped!

Genus is the classification one more general up from species.  Two species in the same genus will be pretty similar - for example wolves and coyotes.  Two things with radically different energy metabolism systems will not be in the same genus.  In fact these different modes of metabolism mean that the creatures using them are so different from each other that they are categorized in different phyla (phylum being the second division after kingdom). Humans are in phylum Chordata with frogs and fish.  Prokaryotes using such different modes of energy metabolism will not be closely related at all.


Are wasps attracted to a sting A little backstory, I was trying to get something that was in a little wooded bit at the back of my garden and stepped on a swarm of wasps was stung 3 times and got out of there but I brought 8 wasps inside and was wondering if they know if you've been stung and are attracted to it and also out of curiosity what would happen to a wasp if it was stung by another wasp

Tackling the second part of the question first: If a wasp is stung by another wasp, that's usually super bad for the wasp in question. Wasps are pretty good about not stinging one another, but occasionally wasps from other communities come in and cause a ruckus, or even predate on other communities of wasp specifically. If a wasp gets stung by one of these, it's about to die horribly, then get eaten.

On the other hand, if it's stung by 'friendly fire', it'll just die horribly. The venoms wasp stingers carry, while merely irritating and only occasionally fatal due to allergies on our scale, are generally pretty lethal to insects, arachnids, and other tiny critters; also, having a huge hole in your exoskeleton doesn't help.

As for the attraction question, the answer is a solid and absolute 'Eh, probably not.'.

Wasps, like a lot of insects, communicate on pheromones and dancing, but on the whole their 'deal' when not hunting is to repel, not kill. They don't care if what they sting gets killed or not; so long as it gets out of their zone of control. While they do issue alarm pheromones and other calls to action, these are not associated with stings in particular, which mostly deliver poison and sharp force trauma, not orders to the swarm.

You'll probably want to clean out the stings in any case, but it's unlikely that your new house guests want anything so much as just going home. Usher them out the door, and they'll be happy as clams.

I was stung this afternoon. I drove home, washed the site with vinegar and was icing it, when out of nowhere a wasp came in through the open window and began to buzz around the part of my arm where I was icing. It landed, walked around for a few seconds, as if it was investigating. It was the oddest thing!


Do aquatic plants have stomata? I am wondering if aquatic plants have stomata or not. I know that non-aquatic plants have stomata to release water(transpiration) and oxygen, and to take in carbon dioxide. Do aquatic plants also have stomata, and if so do they take in water through their stomata? If water is taken in through their stomata, wouldn't other substances such as dissolved salts get in the plants vascular system too? Does the aquatic plant use this salt or remove it, and how would they remove it?

Note: I am talking about fully submerged aquatic plants such as kelp.

According to the book Stomatal function (Zeiger et al, 1987), many aquatic angiosperm plants have stomata (since they have evolved from terrestial plants), while some have reduced or complete loss of stomata.

However, the book also states that:

  ...aquatic plants living underwater are devoid of stomata. Leaves that float in water, which are common in ponds, have stomata on their upper surfaces but lack them on the surfaces in contact with water.

No

First of all, stomata is of course important for gas exchange and also water conservation. Well, clearly, water conservation isn't needed! Also, gases can diffuse relatively easy in water so gas exchange using stomata isn't needed.

Technical notes

Second of all, technically organisms like kelp are thalloid plants. They are in separate kingdoms. Kelp is a brown algae, placed in kingdom algae in laminariales order of class phaeophyta. They does not contain any kind of vascular or conductive tissue as their plant body is thalloid.


Why deoxyribose for DNA and ribose for RNA? Why is DNA made out of deoxyribose and RNA made of ribose? Why can't they both use ribose or deoxyribose? I think that the deoxyribose gives an advantage in storing genes, the job of DNA and ribose is better dealt with outside the nucleus...but why?

Nice question which leads to the fundamentals of DNA and RNA.

DNA (Deoxyribonucleic acid) is the core of life in Earth, every known living organism is using DNA as their genetic backbone. DNA is so precious and vital to eukaryotes that its kept packaged in cell nucleus, its being copied but never removed because it never leaves the safety of nucleus. DNA directs all cell activity by delegating it to RNA. RNA (Ribonucleic acid ) have varied sort of biological roles in coding, decoding, regulation, and expression of genes. RNA carries messages out of the cell nucleus to cytoplasm.

  The structure of RNA nucleotides is very similar to that of DNA nucleotides, with the main difference being that the ribose sugar backbone in RNA has a hydroxyl (-OH) group that DNA does not. This gives DNA its name: DNA stands for deoxyribonucleic acid. Another minor difference is that DNA uses the base thymine (T) in place of uracil (U). Despite great structural similarities, DNA and RNA play very different roles from one another in modern cells.

  http://exploringorigins.org/rna.html

RNA has three main characteristics that differs it from DNA

RNA is very unstable and decomposes rapidly.
RNA contains Uracil in place of Thymine
RNA is almost always single stranded.

DNA and RNA use a ribose sugar as a main element of their chemical structures, ribose sugar used in DNA is deoxyribose, While RNA uses unmodified ribose sugar.

Ribose and Deoxyribose

  From the fig above we can see that the principal difference between
  the two molecules is the presence of OH in ribose (2' tail) and absence
  in deoxyribose. There is a difference in one Oxygen atom as the name
  stands de-oxy ribose. Both Ribose and deoxyribose have an Oxygen(O)
  atom  and a Hydrogen (H) atom (an OH group) at their 3' sites. The OH
  groups are very reactive in nature, so the 3' OH tail is required for
  phosphodiester bonds to form between nucleotides in both ribose
  and deoxyribose atoms.

Answer

DNA is such an important molecule so it must be protected from decomposition and further reactions. The absence of one Oxygen is the key for extending DNA's longevity. When the 2' Oxygen is absent in deoxyribose, the sugar molecule is less likely to get involved in chemical reactions( the aggressive nature of Oxygen in chemical reactions are famous). So by removing the Oxygen from deoxyribose molecule, DNA avoids being broken down. In an RNA's point of view the Oxygen is helpful, unlike DNA, RNA is a short-term tool used by the cell to send messages and manufacture proteins as a part of gene expression. Simply speaking mRNA (Messenger RNA) has the duties of turning genes ON and OFF, when a gene needed to be put ON mRNA is made and to keep it OFF the mRNA is removed. So the OH group in 2' is used to decompose the RNA quickly thereby making those affected genes in OFF state.

Finally, the ribose sugar is placed in RNA for easily decomposing it and DNA uses deoxyribose sugar for longevity.

  References

  Flesh and Bones of Metabolism -  Marek H. Dominiczak

  Genetics For Dummies -  Tara Rodden Robinson

Basically, it is because DNA is so hydrophobic that it does not substantially catalyse reactions in aqueous solutions.

RNA is less hydrophobic and therefore more able to catalyse aqueous reactions, but the same reactivity means that it is more susceptible to degradation and so less suited than DNA to the storage of genes.

RNA is more polar and therefore less hydrophobic than DNA because of the increased polarity of the extra hydroxyl group in ribose compared to deoxyribose.

This means that DNA is more stable than RNA, because the strands are harder to separate because they are more attracted to each other than the surrounding water. Because it is more stable it is more suited to storing genetic sequences with less degradation than RNA.

But because DNA is so stable it requires a substantial amount of machinery just to separate and keep separated the strands when they are needed. It is therefore unlikely DNA was the original genetic material that came about via much simpler prebiotic chemistry.

RNA being more polar is easier to separate. It also unlike DNA can actually catalyse a wide variety of reactions requiring only the RNA and some prebiotic chemistry such as metallic ions or simple fatty acids.

For instance the group I intron can catalyse single electron transfer in the presence of Iron (II) ions. And it can catalyse its excision from a section of RNA with Iron (II) or more commonly magnesium ions.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3365117/

In fact in almost every highly conserved biological process you will find remanent RNA chemistry if not small pieces of RNA held by proteins doing the heavy lifting. This leads to the RNA world hypothesis, which posits that RNA emerged before DNA and before proteins.
https://www.youtube.com/watch?v=U6QYDdgP9eg

But being easier to separate RNA is more susceptible to degradation by aqueous reagents, and being less stable is less suited to the storage of genes without degradation. So if an organism found a way to turn its RNA to DNA for storage and back again it would have a significant selective advantage.

Such a mechanism might be as simple as protein or ribozyme that could preferentially hold DNA in contact with RNA. Then the normal mechanisms of strand ligation could work both to produce DNA from RNA templates and RNA from DNA templates.

Over time there would tend to arise specialised versions to do each task, but each building on the original holding mechanism, which itself could have built on the ligase mechanism. Today there are a number of highly related small DNA and RNA binding RNAs involved in many analogous processes. Search for RNA Structure, Function and Recognition by Anna Marie Pyle on iBioseminars.

I would link some more, but I don't have the reputation. But see also "The Origin of the Genetic Code" by cdk007 in the same series. Also there is an excellent 3 videos on abiogenesis, RNA and fatty acid vesicle "protocells" by Jack Szostak on ibiology. Just search for them.


Looking for source: Biologic reactions of people saying "no" Searching for this topic is incredibly tedious because the word "no" is the main point of interest and I always end up on sites saying how "saying no is good for your health" but I am looking for the medical evidence of this claim.
I remember very faintly hearing about measurable physical effects on a person in a situation where this person says the word "no" to something.
There was an experiment where scientists (I suppose neuro-scientists?) were able to measure the effect of saying "no". Colloquially speaking the body was "closing" in a sense that the person went in some unconscious defence mode, stress levels were rising, change in muscle tone were measurable etc.
When I also remember correctly these effects were measurable even without exposing the person to a specific situation. Just saying "no" wholeheartedly triggered those effects.
Did someone hear about this one? I am looking for any clue to get more information on that.
Edit: I add to the excellent hint from Vadim: I am indeed looking for a credible source where experiments were conducted in a controlled manner and not someone sticking electrodes on people in the mall :D. And I also think this experiment would be hard to do right in the first place since you basically would have to deprive the people from any external stimuli which by itself would probably also already cause side effects.

Most of the claims that "saying no is good for one's health" are grounded in psychology. In other words, they are  not experimentally verifiable. Likewise, health here refers not only literally to physical health, but also to psychological health, which in itself is something hard to define.
Surely, in situations of high stress saying "no" can actually result in some measurable responses, in which case it can be studied within the context physiology and neuroscience. However, this would address only a small part of the situationd covered by the original claim - discarding any effects on psychological health as well as long-lasting effects on the physical health.
To summarize: for a scientific study the claim needs to be made more specific, i.e., apply to well-defined situations and responses.
Disclaimer
I feel that a clarification is needed, lest what I wrote above is interpreted as a negative view of psychology.
I am not claiming that all of the psychology is outside of the scientific method, but a big part of it is - at least outside of being possible to study in a laboratory setting. And this is by no means unimportant part, in terms of the role it plays in our society. While words not scientific often carry negative connotation, in practice any scientist should recognize that scientific method has its limitations - many phenomena (psychological, social, economic, etc.) are not sufficiently reproducible and controllable to study experimentally, yet too important to dismiss.


Why does the heart use lipids (and not glucose)? Fetal hearts use glucose as their primary metabolic substrate.  Adult hearts use free fatty acids, which are less efficient (require more $O_2$ to synthesize the same amount of ATP); however, during cardiac failure, the heart can switch to glucose utilization.  Why doesn't it just use glucose all the time?

Lipids require more oxygen to burn, but also they are cheaper to store (since they have great calorific power than carbohydrates and they're hydrophobic, thus not requiring water for their storage). The body can store so much lipids that it becomes an almost everlasting energy source (A normal adult have enough energy stored as fat to allow basal metabolism for weeks to months), which cannot apply to glucose. If fat is not present, glucose would have vanished from the body long time ago. Glucose levels must be maintained at a certain level, because it's the main energy source for the brain (which cannot use lipids ). The brain can use ketone bodies (product of fat oxidation) as a last resort.

For all the previous reasons, the heart (and many other organs, like the liver) uses fat while possible. If possible just means when not starving to death and with sufficient oxygen supply. This second condition doesn't apply to heart failure. In this case, oxygen supply fails and the tissue switch to glucose just because they can use it without oxygen (glycolysis and lactic fermentation).

The usual explanation is that glucose is potentially dangerous because there is always a chance glycolysis will run too fast and produce lactic acid.  While lactic acid buildup is no big deal for a skeletal muscle, lactic acid build up in the heart can affect the ion channels and hence the heart rhythm.

Fuels for the heart are fatty acids, ketone bodies, and lactic acid taken from the blood.  Evidently when the source of lactic acid is the blood, the heart does not take it up any faster than it can convert it to pyruvate (and then to AcCoA, etc.)

Since aerobic metabolism is so important for the heart, is has a high content of mitochondria.


What implications has the missing 2'-OH on the capability of DNA to form 3D structures? The chemical difference between RNA and DNA is the missing 2'-hydroxyl group in the nucleotides that build DNA. The major effect of that change that I know of is the higher stability of DNA compared to RNA. But I'm wondering whether this difference has significant implications for the ability of DNA to form compex, three-dimensional structures.

RNA is known to be able to from complex tertiary structures and function as ribozymes. It clearly has the ability to form a wide range of structures and can catalyze a variety of chemical reactions.

As far as I know, there are no naturally occuring catalytic DNAs known. But a number of synthetic DNA enzymes have been created in the lab, so it is generally possible for DNA to form catalytic structures (see Breaker and Joyce 1994 for the first created DNA enzyme).

I'm wondering whether the missing 2'-OH means that DNA has less potential to form complex structures compared to RNA? I imagine it changes the ability to create hydrogen bonds, but I don't know if it would significantly decrease the potential structures that DNA could adopt.

Breaker RR, Joyce GF; (December 1994). "A DNA enzyme that cleaves RNA". Chem Biol. 1 (4): 223–9

To make sure I'm not comparing apples and pears, my (attempt to) answer the question will be broken into two parts: comparison of single-stranded nucleic acids and double stranded ones.

Single stranded DNA and RNA

Both DNA and RNA can form single-stranded complex tertiary structures in which the secondary structure elements are associated through van der Waals contacts and hydrogen bonds. The presence of a 2'-hydroxyl group makes ribose ring prefer different conformations than deoxyribose in DNA. Also, since 2′-OH moiety is both a hydrogen donor and acceptor, it provides RNA with greater flexibility to form 3D complex structures and stability to remain in one of these conformations. As Aleadam notices, this paper shows that tRNA and its DNA analog form similar tertiary structures though tDNA is not as stable as tRNA:

  Therefore, we submit that the global conformation of nucleic acids is primarily dictated by the interaction of purine and pyrimidine bases with atoms and functional groups common to both RNA and DNA. In this view the 2-hydroxyl group, in tRNA at least, is an auxiliary structural feature whose role is limited to fostering local interactions, which increase the stability of a given conformation.

These authors also show that at least one loop in the tDNA analog is more susceptible to cleavage by a restriction endonuclease. In this region the tRNA has a water molecule hydrogen bonded to 2'hydroxyl group.

I was not able to find more of such interesting comparisons in the literature.

Double stranded DNA and RNA

Both DNA and RNA can form double-stranded structures. Again, sugar conformation determines the shape of the helix: for DNA helix it's usually B-form, whereas helical RNA forms A-geometry under nearly all conditions. In RNA helix we find the ribose predominantly in the C3’- endo conformation, as 2'-OH stericly disfavors the C2'-endo conformaion, necessary for B-form geometry.

Physiological significance

dsRNA and ssDNA often provide a signal to the cell that something is wrong. dsRNA is of course seen in normal processes like RNA interference but it can also stop protein synthesis and signal viral infections (cf. double stranded RNA viruses). Similarly, ssDNA is much more prone to degradation than dsDNA, it often signals damage of DNA, or infections from single stranded DNA viruses and induces cell death. Therefore, due to their functions, under normal conditions DNA 3D structure is mostly a double-stranded helix, whereas RNA has a single stranded, "protein-like", complex 3D structure.

the OH group in the two position acts a as a nucleophilic catalyst for the cleavage of RNA or of DNA if it had such a group. Since DNA needs to stay intact throughout the life of a cell it would be disastrous if it were cleaved because of the 2'OH group. RNA on the other hand is rapidly cleaved as needed by the cell without detrimental consequences to the cells genetic code so it can have an OH group.-chem major


What is most simple eukaryotic genome? Expressed in number of Base Pairs or Bytes, about how large is the simplest eukaryotic genome?

How much of this is 'junk-DNA' (non-coding)?

You asked about eukaryotes. The genome of the yeast Saccharomyces cerevisiae is 12.2 Mb.

The genome of the smallest free-living eukaryote, Ostreococcus tauri (a unicellular green alga) is 12.6 Mb

There are smaller eukaryotic genomes, but these are not free-living organisms they are intracellular parasites.

According to this:
http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/G/GenomeSizes.html
The shortest DNA of a individually living cell is that of Mycoplasma genitalium at about 580000 base pairs. -But it's not eucariotic!


What is the name of this whorled-leaf tree in India? Location: South India

Month: June

Season: Rainy

Branch Distribution:

Leaf of the tree:

Bucida molineti also called geometry tree


Is there a way tell apart dinosaurs from similar extinct reptiles? When I was a child, I thought I knew what a dinosaur was. But, as I grew older, I was told that many of the extinct species that I thought were dinosaurs (dimetrodons, pterosaurs, plesiosaurs, etc.) were not in fact dinosaurs. Is there a reasonably quick way for a lay person to tell apart true dinosaurs from non-dinosaurs without taking up an in-depth, species-by-species study of paleontology?

There are several defining morphological characteristics of dinosaurs. Including their ankle structure and perforated acetabulum, Aka the hole in their hip goes all the way through, as well as a few other minor features. These combined makes it literally impossibly for a dinosaur to take on a sprawling pose without breaking hind leg in many places, this is why you will often see an erect posture given as the reason, but that is a product of these feature not the defining feature itself, there are many ways to achieve upright posture.

Now of course we are moving away from purely morphological definitions, cladistically dinosaurs are defined as The last (most recent) common ancestor of Triceratops horridus and Passer domesticus (common pigeon), and sometimes Diplodocus carnegii as a third, and all of its(the ancestor's) descendants.

A more superficial quick and dirty method is if it is a pterosaur or lives in the ocean it is not a dinosaur, If its limbs sprawl it is also not a dinosaur. I should also include this guys work, since he attempted to create a complete cladogram of every dinosaur, so you can visualize the group.

Yes, the legs of dinosaurs are directly beneath their bodies. This is more efficient that the sprawling stance of lizards, crocodilians, pelycosaurs, and other mammal-like reptiles. It is likely no coincidence that another successful group, mammals, also have their legs directly beneath them. Also, as far as I know there were no fully marine dinosaurs.


Bilirubin metabolism and UGT1A1 inhibition in human vs. monkey? In human UGT1A1 seems to be the only relevant enzyme to glucuronidate unconjugated bilirubin into excreted forms. Is the pathway the same for e.g. the Cynomolgus monkey (Macaca fascicularis) in vivo? In case UGT1A1 is potently inhibited are there any other potential enzyme to metabolise/glucuronidate unconjugated bilirubin in monkey? Furthermore, bilirubin is analytically challenging in UGT1A1 inhibition studies in vitro. Estradiol (3-glucuronidation) has been used as a specific substrate for human UGT1A1. Do you know any substrates known to be specific for monkey UGT1A1?  Any reference would be highly appreciated.

UGT1A1 is common among most mammals that produce bilirubin (rats too). I haven't seen any evidence to suggest an alternate pathway in mammals of bilirubin metabolism. Look into gilbert's syndrome patients (they have a SNP which is a mutuation that causes UGT1A1 to be less efficient and thus a rise in plasma unconjugated bilirubin).

Also, bilirubin analysis from plasma/tissues is fairly straight forward with HPLC or LCMS assays. UGT1A1 inhibition in vitro however, is still a challenge. I think the trick will be to use CRISPR to knock it out.


How correlated is the chirality of different molecules? In astrobiology, a proposed way of testing whether life found on another world is alien or originates from Earth is to determine the chirality of its molecules. This is of course only useful when the biochemistry is similar enough that one may suspect contamination.
But this test has a weakness. While different chirality can confirm alien origin, similar chirality does not exclude alien origin.
To mend this, a plausible idea is to cross check the chirality of a wide range of compounds. A false positive suggesting Earth origin would then have an exponentially smaller chance to match every single compound tested.
...or so I hope.
The issue is that I fear various chiral compounds do not have statistically independent default chirality. For instance, common biochemical pathways may produce one compound from another, leading the chirality of the first molecule to directly determine the chirality of the second.
I'm looking for a high level perspective: Does the chirality of a single compound more or less determine the chirality of all other compounds in an entire biochemistry, or are there a great number of compounds that have an arbitrary default chirality compared to others?

Hypothetically if an alien species were found , and if they contained similar biochemical polymers (DNA with A,T,C,G , Protein with 20 Amino acids etc) then we MAY be able to conclude that they share an origin with us. (Just similar chirality does not necessitates the theory of same origin)

Does the chirality of a single compound more or less determine the chirality of all other compounds in an entire biochemistry?

Yes. As Chiral molecules are almost always produced/purified from chiral medium (containing other chiral molecules and/or chiral physical attributes e.g. polarized light).
Therefore (Assuming that the reaction is enantioselective and you want pure chemical with a specific stereochemistry) the configuration of the chiral center of a new molecule does depend on the reagent chirality. Still this relation is not constant and differs from one reaction to another. For instance textbook SN2 reaction leads to inversion of configuration while Williamson ether synthesis reaction maintains the chirality.
A non-racemic mixture of a chiral compound is resulted from previous non-racemic mixture and so on. therefore the stereochemistry of the first non-racemic mixture determined the S/R , L/R ,(-/+) chirality of the entire life per se whose identity may never be fully understood.

Biologic reactions preserve chirality whereas non-biologic reactions generally do not (although there are examples of rxns where chirality is preserved )
I think this strategy would work for comparing  biomolecules with multiple chiral centers. For example, from an IUPAC perspective, D-glucose is (2R,3S,4R,5R)-2,3,4,5,6-Pentahydroxyhexanal and simply among aldoses  & ketals , finding a single biomolecule (not just carbohydrates,) with multiple chiral centers where a single carbon involves a different chiralty than one used by life on earth, would highly suggest that non-earth originated life was responsible.


How long does it take for dopamine to reach normal levels after a significant drop? The building block sequence for is: Phenylalanine << Tyrosine << L-Dopa << Dopamine. It’s produced in only a few, very specific regions: Substantia Nigra and the Ventral Tegmental Area. Although, on average does this take minutes, hours, days, weeks? And does releasing it between synapses or something else for normal activity affect the time?

Ultimately, I am trying to find a graph of the average anergia level after sex. Or similarly, dopamine levels after orgasm. Most of the research I have come across is about disorders or is too general. Also, there are informal articles and graphs of dopamine levels, but they very widely and are not sourced.

I can see a couple of problems in the question:

First problem, you assume that anergia (not sure that's how you call being tired) after sex is caused by dopamine depletion, I'm not sure this is the case or that lack of dopamine has been related to anergia at all. We know from Parkinson patients that Dopamine is related with action initiation (http://www.nature.com/nature/journal/v466/n7305/abs/nature09263.html) not necessarily with lack of energy or motivation.

Second problem, depletion (the term you originally used) means no more dopamine is system, either because you block it somehow (antagonist), you block its receptors (receptor antagonist) or you block one of the precusors involved in synthesizing it eventually depleting your reserves. "Significant drop" needs to be quantified.

Dopamine (DA) synthesis is an ongoing process, and DA is an essential neurotransmitter / neuromodulator in the brain just like Serotonin (more on that later). This means that it probably has different roles. One phasic referring to its neurotransmitter properties and one tonic referring to its global levels in the brain and how it modulates ongoing synaptic activity.

Normal activity does not deplete DA, and yes, no matter how crazy you think you are, sex is considered normal activity. You can obviously have variations of basal levels of DA depending on your activity but they are way removed from the depletion criteria.

Furthermore, the brain is very parsimonious in its synthesis efforts, it has specialized molecules that recover neurotransmitters that where unused from the synaptic cleft, these molecules are appropriately called reuptakers.

Now to attempt to answer your question considering the problems:

I don't know about DA but I do have some experience with serotonin depletion.
Serotonin (5-hydroxytryptamine, 5-HT) is synthesized from tryptophan that you cannot produce endogenously. Lucky for us that tryptophan is in almost every food we eat which means that there is no lack of it.

You can, in experimental conditions, ask people to drink a glass of a very disgusting liquid that will bind to your tryptophan preventing it from being used in new 5-HT synthesis. It takes approximately 4-6 hours for it to work (e.g. http://web.stanford.edu/~knutson/ans/bjork99.pdf methods section), which means that in 5 hours you used up all your reserves of 5-HT. This meansthat your "refilling" process would be about the same time  in order to get to pre-depletion levels (you might be able to be in a functional regime before that if you ignore the reserves part).

So from this 5-HT example I would say that unless something is very different in the case of DA to recover from depletion it would have to be in the hours time frame.

Another way of looking at it can be looking at the half-life of the molecule which gives you an idea of how much time it lives. This can be used to calculate how much production there has to be to maintain a level of X. The turnover is the amount of time that it takes to, well, turn over, so replace DA in the system that should be in the same order of magnitude as coming back from a depletion experiment.


What is the name of this bush with red fruits? I have seen this on Corsica (Island of France):

It is Arbutus unedo, called "strawberry tree" in English, "arbousier" in French and "medronheiro" in Portuguese. The fruits are ripe around October or November. They are full of little seeds, but if you bear the annoyance, they can be quite tasty. They are used to distill an alcohol in Portugal.

The fruit looks like lychee (Litchi chinensis). But this was a hasty guess and now I see that there is a much better answer here!

(image from Wikipedia)