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Lab marker for labelling cell culture plastics?
I am a lab manager trying to ask other lab biologists what brand/make of markers their labs use for labeling tissue culture plastics, which need to be repeatedly wiped down with 70% ethanol to maintain sterility. (Most "permanent" markers wash off in 70% ethanol.)
I have been looking for an equivalent to the Sharpie Industrial Extra-Fine point marker, which seems not to be on the market anymore. The supposedly solvent-resistant Fisher extra-fine point marker leaves almost no trace when wiped with ethanol.
Does anyone have suggestions?

I'm voting to close this question as off-topic because recommendations for marking pens can by no stretch of the imagination be considered a question about biology.

I think the question is reasonable because it is asking for recommendations on lab materials which only a biologist would be able to make.

Yes, @David, to clarify: biologists use 70% ethanol to wipe down their cell culture materials in order to maintain a sterile environment, but most "permanent" markers wipe off under those conditions. I am a lab manager trying to ask other biologists what pens their labs use for this biology-specific application.

I agree. This question, though seemingly wayy off topic, is completely valid here. It has the appropriate [tag:lab-techniques] tag. @Ema, to avoid more challenge to your question, perhaps you could edit to add a bit more biology context. I think adding your " I am a lab manager trying to ask other biologists..." sentence from your comment to the start of your question would be good :).

I routinely use 70% ethanol and/or IPA to wipe off plastics written on with Fisherbrand fine-tip marking pens and I find they don't come off easily even after multiple sprays. As long as the marker has had ample time to dry. The sharpie industrial "solvent resistant" markers come off immediately.
So here I have a Corning 250mL bottle, and 3 brands of marker:
Fisherbrand fine-tip marking pen (above)
Sharpie Industrial (above)
Sakura microperm ultrafine-tip
The Sakura markers explicitly state they wash off w/ alcohol but I like the tips for flow tubes and eppendorf tubes. I sprayed the marker with 70% ethanol, let it sit for just a few seconds then used a Kim wipe to clean it off. Fisherbrand, for me, just works the best (excuse my handwriting!).

I've resized the images and put them on less lines so we don't need to scroll for what seems like miles. Feel free to roll back.

Thanks for the input. Unfortunately, I'm in the market for extrafine. The Fisher fine tips work well, but the extra fines come off.

@Ema I see. You might find some luck testing VWR's histology markers, which come as ultrafine and out of necessity have to resist histology solvents. I have not tested these myself. The downside is they apparently don't write well on smooth surfaces, only frosted parts.

This is hardcore going to come across as a SPAM answer, but I simply did a Google search:
Laboratory Marking Pens from Ted Pella

Statmark Pen™: resistant to formalin, ethanol isopropanol and xylene
Secureline® Marker: water resistant; autoclavable; not suitable below 0°C (32°F)
Secureline® II / Superfrost: resistant to xylene, ethanol, acetone and formalin; service temperature -15°C to 100°C (5°F to 212°F)
You can try a Sample Pack of all 3 for $8 USD to see which you like the best.

@Ema Try them out and let us know how they work! (Alternatively... Has anyone used these that could report on their efficacy?)

I have tried both of those Securelines, but the Extra Fine one doesn't hold up. As stated above, I'm particularly interested in other users' advice on products they have tried and rely on.

@Ema Bummer. Well, don't miss the link in my answer to the sharpies I still found on sale for you! :)

Those are not the correct Sharpie product, but feel free to repost if you find a source for Sharpie Industrial Extra Fine.

@Ema weird. They changed links on me. Now the correct page lists them for sale for $700! 0.o  ... I'll keep my eyes and ears open for ya!

Yeah, I've seen that too... :(


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What is this plant & it looks like USA tree " Carya ovata"?
I saw this tree in India. It was so fascinating because its leaf looks like Carya ovata, which only grows in the USA & Canada according to Wikipedia:

Carya ovata, the shagbark hickory, is a common hickory in the Eastern United States and southeast Canada.

Is it really Carya ovata or something else?

This looks nothing like Carya ovata.

Also, please add close-ups of the leaves, (supposed leaflets) and trunk if possible for a better chance at a correct ID

Are the branches opposite or alternate?

source: Stack Exchange

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sort: votes


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Can a mother somehow positively affect fetus during pregnancy?
My mother keeps telling me that I like to study and have a predisposition to it because she was a student when she was pregnant. I highly doubt it, because I can't find any logic in these words.
I heard that a lot of mothers try to do something to positively affect their fetuses. For example:

Listening to classical music.
Learning something.
Singing or playing musical instruments.

Can these activities somehow affect a child or is it just a myth?

why the downvote??

You should reduce your question to a single clearly defined question like does listening while to classical music in the womb increase the kid's IQ? Your three questions are too broad. The title question is particularly broad and I suppose the fact that the mother give nutrients to the foetus would be enough to answer yes. I am voting to close as too broad (I was not the one down voting but I can understand the down vote).

I don't think the question is about any specific activity; those are just examples. The question is can the behaviour of the mother during pregnancy have an effect on the fetus.

@canadianer Like smoking, drinking alcohol, not feeding yourself correctly, etc.... Shall we make a short list like that and post it as an answer?

@Remi.b "Can a mother somehow positively affect fetus during pregnancy?"

@Remi.b No, you should not list everything. Especially not things that are obviously not in the spirit of the question.

@Artmal Not smoking is a way to positively affect the foetus.

@canadianer It is hard to tell what is in the spirit of the question without a accurate definition. I still think the quesiton is too broad and the OP should narrow down to a specific behaviour of interest. It is of course my personal opinion. If other users feel like it is answerable, they can give it a shot.

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How do you differenciate between the eukaryotes and prokaryotes?
I wonder how we differentiate between the eukaryotes and prokaryotes.
Eukaryotes:

Eukaryotes (also spelled "eucaryotes") comprise animals, plants, and
   fungi—which are mostly multicellular - as well as various other groups
  that are collectively classified as protists (many of which are
  unicellular).

Prokaryotes:

Prokaryote (also spelled procaryote) comprise any organism that lacks a
  distinct nucleus and other organelles due to the absence of internal membranes. Bacteria are among the best-known prokaryotic organisms.
  The lack of internal membranes in prokaryotes distinguishes them from
  eukaryotes.

Isn't there any other method to know what organisms are eukaryote or prokaryote?

There are lots of ways to distinguish between eukaryotes and prokaryotes, as listed by microbiologynotes.com:
Difference:             Eukaryotes:                Prokaryotes:
-------------------------------------------------------------------------------
Size                    > 5µm                      1-2µm by 1-4µm
Nucleus                 Nucleus with nuclear       No true nucleus; nucleoid
                         membrane
Complexity              Usually multicellular      Unicellular
Chromosome              Multiple linear; histones  Usually single circular;
                                                    no histones
Cell Division           Mitosis, meiosis           Binary fission
Reproduction            Involves meiosis           No meiosis
Zygote                  Diploid                    Merozygotic
Genes                   Expressed individually     Operons
Gas vacuoles            No                         Possible
Mesosome                Yes                        No
Ribosome                Found on membranes         Distributed in cytoplasm
Mitochondria            Usually present            No
Chloroplast             Possible                   No
Cell wall               Simple if present          Freq. present, complex
Endoplasmic Reticulum   Possible                   No
Golgi apparatus         Possible                   No
DNA usage               Transcription in nucleus,  Transcription at the same
                         translation in cytoplasm   time as translation
Duration of cell cycle  Usually long (hours)       Usually short (<1 hour)

N.B.: I have used the list on microbiolgynotes only as an outline, editing as needed.  For instance, Mitochondria is not necessarily present in eukaryotes, neither are chloroplasts.  Also, I have not included everything, since I do not presently have the time to verify everything.

I would like to add several comments. "Mitochondria is not necessarily present in eukaryotes" – this is not entirely true, even those eukaryotes that lack complete mitochondria still posses the remnants. "Ribosomes: Distributed in cytoplasm" – there are several notable exceptions (most notably Gemmata sp. ). "No true nucleus" – again, some members of the PVC group (Gemmata being the most studied of these), enclose the DNA in a membrane-bound compartment. "Genes: Expressed individually/Operons" – some eukaryotes have operons and not all genes are organised in operons in bacteria.

"Cell Division: Binary fission" – a ton of exceptions, including mycelial division and eukaryote-like budding. "Duration of cell cycle: Usually short (<1 hour)" – this is only true for some copiotrophs. "no histones" – some Archaea have true histones.

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Why is secretin sensitive to acid?
My textbook says, secretin secretion is triggered by the presence of acidic chyme in intestine.
But why is secretin sensitive to acidic environment? I checked the wikipedia page of secretin and found no related information.
Is there some mechanism for secretin to secrete in presence of acidic chyme?

The exact mechanism by which secretin is released is still not known.

The mechanism by which acid brings about secretin release is not fully understood but probably involves acid sensing ion channels of the Trp family present in the brush border of S-cells.

Physiological reason for susceptibility to acid: It is because this hormone acts on pancreas and increases the secretion of bicarbonates to increase the pH. It also reduces gastric motility thereby allowing longer digestion within the stomach. So, it effectively prevents deterioration of duodenal mucosa and helps in efficient absorption of lipids by increasing ph in duodenum which is required for better action of lipases. So, its secretion is induced by increased acidity from chyme (so that it can increase pH).
Thus, we can conclude that secretin is acid sensitive.

Source: https://www.pancreapedia.org/molecules/secretin

You forgot to connect your last paragraph to "thus it is acid-sensitive" (its not easy to draw this conclusion from your paragraph). Anyways, +1! ;)


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Best methodology to compare computed phylogeny tree with taxonomy?
I have computed a phylogenetic tree using an alignement of sequences, and I would like to :

Compare it to the "known" taxonomy (uniprot/ncbi which I know is not
the most up to date one) and extract a metric of how "divergent" it
is.
[Optional] Visualize the differences (I can probably come up with a
solution for that one, but if someone knows of a nice tool to do so
?)

What are the best metrics / tools / methodologies to do such a comparison ?
Thanks !

Take a look at the ape package in R. It has a function called cophyloplot which allows you to visualize two trees like so:

Which is well described in this question (also the source of the image).
There is also the dist.topo function which produces a metric which describes the topological distance between two phylogenetic trees. I don't know if this is what you mean by "divergent" but I hope it helps.


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Why do erythrocytes have no MHC1 but platelets do?
Red blood cells do not have a considerable number of MHC1 through their membranes, and that's explained by them not having a nucleus. But why do platelets have MHC1s if they have no nucleus either? I don't think that lifespan is a good enough explanation since that would mean young red blood cells have MHC1s and old platelets don't, since the latter can last over a week in circulation. Megakaryocytes do have MHC1s, but that means nothing, since red blood cell percursors also have them.

There's actually a good answer to this on Quora.


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Significance of lip end curve
What is significance of curve at point where lips meet, how it is determined and what effects it has on attraction and other factors? For some people it is a downward curve, for others it's an upward curve, while for some it is straight.
Is it genetic?

I don't think it can be called as a trait, since that region is highly mobile and changes according to emotions. But its well known that it gives an impression of downward curve in oldage.

@JM97 it is my observation that when lips are closed some people do have upper curves while most has downward, i thing upward and straight one is more attractive, so may be it is a trait. I checked on my self too, you can check on urself too.

this may help you:http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003375


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What would be the Hardy-Weinberg equilibrium condition for a population of haploid organism?
What would be the Hardy-Weinberg equilibrium condition for a population of haploid organism?
Would it always be in Hardy-Weinberg equilibrium?

@Remi.b
campbell biology says that a population of diploid organisms is at hardy weinberg equilibrium only when
p^2 = fraction of population with homozygous dominant organisms
q^2 = fraction of population with homozygous recessive organisms and
2pq = fraction of population with heterozygous organisms
if this relation is not held (between the calculated and observed values) then it can be concluded that the population is evolving
This is how I understood hardy weinberg principle

A) The $p^2$, $2p(1-p)$ and $(1-p)^2$ relationships hold only for bi-allelic loci in diploid populations. It is not a general result. It is obvious that, the frequency of heterozygotes in a haploid population cannot be any different from 0. B) The assumptions of HW equilibrium include absence of selection, absence of migration and infinite population size (hence absence of drift). If a population fits these assumptions, then the population is not evolving, this is true.

What is HW rule?
HW rule is a rule allowing one to compute genotype frequencies from allele frequencies and vice-versa. See Solving Hardy Weinberg problems and eventually Assumptions of Hardy-Weinberg rule for more information.
HWr in haploid organisms
In haploid individuals, the genotype frequencies and the allele (or haplotype) frequencies is the exact same thing! This is because the genotype is a simple haplotype. In other words, once you have the allele frequency, you necessarily have the genotype frequencies without need for any calculation. We can consider the haploid organism would display a special case of HW rule, where there is no assumption and where
$$p = f_{A}$$
$$q = f_{B} = 1 - f_{A}$$
, where $f_{A}$ is the frequency of the genotype carrying the allele A and $p$ is the frequency of the allele A. $f_{B}$ is the frequency of the genotype carrying the allele B and $q$ is the frequency of the allele B.


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Do any dogs have blue iris - not just sclera?
I was looking in to the question of whether any dogs in fact have "blue eyes"...
A quick search gives plenty of information on and images of dogs with blue sclera and black iris.
Every "blue-eyed" canine I know of personally or could google up has black iris and blueish sclera.
It is unclear if any dogs have blue iris.
(BTW there are many popular articles on the "four typical reasons" that canines can have blue sclera).
Humans with "blue eyes" of course have blue iris / white sclera.  But the only dogs I have found with "blue eyes" in fact merely have blue sclera and black iris.
I did find a couple of poorly-written lite info sites that mention blue iris, but appears to be basically a typo, the articles appeared to mean to refer to blue sclera -- I cannot find any actual scholarly articles on the issue --
(I"m sure, everyone on this site knows that regarding humans with "blue" iris, it's not "really" blue, but a Tyndall effect. Popular article on that.)
And don't mention cats - it's commonplace that cats have "blue eyes" but every image I've seen is of a feline with blue sclera, and black iris. One could ask, do any felines have blue iris?
In short my question is ... do any canines have blue iris??

What evidence have you that blue-eyed dogs actually only have blue sclera? Do you suppose their irises to be colorless then? That would make their irises red, as albino eyes.

Hi Anon!  "blue-eyed" dogs have black iris, as I think I mention in the question.  My only evidence for this is that every "blue-eyed" dog I have ever seen has blue sclera / black iris, and every photo I have been able to "google up" is blue sclera / black iris.  Further, I have exhaustively googled "dog with blue iris" and there are none I could find -- hence, I am asking the experts!!!

I think you are confused. The iris is colored, the pupil is black. The sclera can be white, tan, or bluish-white. I myself have never seen a black iris in dogs or humans.

I think you are confused. When dogs look straight at you, their sclera is not visible. What you are seeing is their iris and pupil.  It is only when they glance off to the side that you can see the sclera of a dog's eye. Humans are pretty much the only mammals where the sclera is normally visible. In a dog, the iris entirely takes up the area which in humans would be sclera.  So malamutes, huskies, etc. will have blue irises black pupils. And pupils aren't actually black, they are an aperture, so the light passing through the lens is not reflected back so it appears black.

@AMR I'd never thought about humans being unusual like that, great thought, I wonder why it evolved - the cooperative eye hypothesis seems plausible at least

Ahhhhhhh!   I was mixing-up the iris and sclera since the iris is so big in dogs!!!!  Nice work, Anon and Amr

Why would anyone down-vote this question?  (I couldn't care less - but why?)

@rg255 Christiaan gave a very informative answer to that question. http://biology.stackexchange.com/a/40680/16651

I have no idea why you cannot find reputable sites that discuss eye color in dogs. Dog breeds with blue eyes should satisfy you; I can't see that they would have any reason to dissemble. In case it doesn't, the references below should. Of course dogs, like humans, cats, and many other animals, can have blue eyes (and by that, I mean irises. Dog irises are not substantially different than human irises. Neither are dog sclerae. They do have a more interesting retina, however.)
This is one of my dogs, a Border Collie, one of several breeds in which complete heterochromia is common. Her right eye is a pale blue, her left is dark brown. Her sclerae are off-white and the conjunctiva are usually somewhat injected; her pupils are black, because they are simply an aperture through which light passes to the retina.

The pupil is large (dilated) because this is a night-time photograph.
Many breeds of dogs have blue-eyed varieties. As with some cat breeds, blue eyes are sometimes genetically linked with deafness.

Blue eyes were positively associated and patches were negatively associated with deafness in the Dalmatian.

(The pink stuff on her forehead and nose is beet juice.)
Deafness prevalence and pigmentation and gender associations in dog breeds at risk
Brainstem Auditory-Evoked Potential Assessment of Congenital Deafness in Dalmatians: Associations With Phenotypic Markers


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Is there a biological mechanism for evolution encoded into our DNA?
Throughout high school, I remember learning about Darwin's theory of evolution as if it were near-fact. But something always seemed wrong about the ideas presented.

Survival of the fittest
Random mutation
Natural Selection

All of these things seem to account for some margin of evolutionary progress, but I always remained skeptical that the extremely complex features of life could have formed from these methods alone, even after hundreds of millions of years.
Here's what I notice:
Any time a species has needed the development of a specific feature to survive, it has developed that feature, and that feature precisely.

I'm going to use this example:
Turtles on an island where shrubbery grew higher up developed longer necks, to reach the leaves.
I imagine that turtle looking up at that food, and sub-consciously wishing to get to it, constantly straining, for its entire lifetime.

It seems plausible to me that we (advanced life) could have a biological mechanism to "write" needed alterations into either our own DNA or our reproductive DNA over time, triggering the very specific evolutionary developments necessary to our survival without relying on random mutation.
My question:
Is this possible? Does any similar mechanism exist that we know of? If not, how can so many specific (advanced) evolutionary leaps be otherwise explained?

You're trying to "bootstrap" your study of this material, and there's nothing wrong with that, but grabbing an article or two would help quickly clear up some of these fallacies (e.g., "Any time a species has needed the development of a specific feature to survive, it has developed that feature, and that feature precisely").

(http://www.amazon.com/Why-Evolution-True-Jerry-Coyne-ebook/dp/B001QEQRJW/ is also a great starting point, for example)

"Any time a species has needed the development of a specific feature to survive, it has developed that feature, and that feature precisely." That's wrong--the history of life is a history of unbelievably numerous failures to develop what was needed. The great majority of all species failed to develop what would keep them alive--that is, they went extinct!  And those who did develop the needed feature often developed a "good enough" version, which is far from "precise".

@Chelonian I'll leave that line to avoid falsifying parts of answers that address it, but for the record, I agree, that was a mistake. "In many cases..." is the wording I should have used.

@jt0dd Even "in many cases..." is, though strictly true, arguably misleading. What about, "In perhaps 0.1% of cases..."? (The number of extinct species "on the internet" appears to be 99.9%, but I'm looking for a reference for it.). And of course, finding those 0.1% of cases that "worked" as reason to doubt evolution by natural selection, it is sort of like being surprised that raindrops would just happen to fall into a shot glass on a field during a long and torrential downpour.

All those turtles looking up at the bushes wouldn't "cause" them to develop longer necks/legs/whatever. What would happen is that over a long time interval small random variations in neck length would give those with longer necks a survival advantage over turtles with shorter necks, so long-necked turtles would survive and reproduce. Over time, continuing random variation in neck length would continue to favor the survival and reproduction of long-necked turtles until all the turtles on the island had longer necks. The key elements are "over time" and "small random variations".

Wow, even comments to this question are long :) Scientist really don't like teleology

This entire answer will be long, so read the short part first, then read the rest if you (or anyone else) is curious. Citations are included in the long section. I can include additional citations in the short section if needed.
Long Story Short
Your question touches on some common misconceptions about how the evolutionary process. Organisms don't "want" to evolve traits. Traits evolve through the biological processes of random mutation and natural selection.
Organisms do not "want" to evolve traits.  (Well, OK, I'd love to evolve an extra pair of hands but that is not possible.) Natural selection works by modifying existing traits. Your turtle can stare all she wants at food out of reach but she will not evolve a longer neck. Instead, natural variation exists among neck lengths of the turtles because of variation of the genes that determine features related to overall boxy size. Those individuals with longer necks may be able to get a bit more food, live a little longer, and reproduce a little more. They will pass along their genes to their offspring, so perhaps more of their offspring will also have longer necks. Over many generations, the turtles may have somewhat longer necks.
A common misconception is that the traits of organisms are precisely adapted for a specific need. They are not, for a few reasons. First, natural selection occurs relative to the current environment. Adaptations that work well in one environment may not be so useful in another environment. Environments are rarely stable over evolutionary time so traits are subject to constant change.
Next, as mentioned above, natural selection can only work on what traits are present. While an extra set of arms would be handy, I am a tetrapod. My four appendages, along with the appendages of all other tetrapods, trace back to our common ancestor. The appendages of all tetrapods are modifications of that ancestral trait.
Finally, organisms haven't "sampled" the entire realm of possible mutations and combinations of mutations. In other words, a certain mutation or set of mutations might actually be able to adaptively improve a particular trait in the current environment but, if the mutations never occur, then the improvement can never happen.
We only need to look at ourselves to realize how imperfectly adapted we are. We get bad backs and knees because our bodies weren't designed to walk upright. We evolved from quadrupedal organisms. This has happened so recently that changes in the structure of our knees and backs haven't yet evolved (and may never).  Search the internet for the "blind spot" eye test. We have a mass of blood vessels in front of the retina of our eyes, which reduces our visual accuity. We often have to have teeth pulled from our jaws because the flattening of our face (relative to our australopithicine ancestors) has shorted our jaws. We don't have as much room for our teeth but we have not evolved a reduced number of teeth.
As for human technology being able to make direct changes to our DNA to improve our adaptability, I would say no. While I do not have the ability to see into the future, the complexity of our genome, and more specifically how genes are regulated, suggests to me this would be a very daunting if not impossible task.  See the long answer below for more on regulatory genes but the gist is that a small set of regulatory genes control most of the other genes (including other regulatory genes). The interactions are extremely complex and we have a detailed understanding of very few of these interactions.  I speculate that affecting one such gene in a "positive" way is very likely to have many unintended negative consequences.
Below are some simple math and other ideas to show you how mutations can lead to the many adaptive traits that you see among the diversity of life on earth.
Long Story

how can so many specific (advanced) evolutionary leaps be otherwise explained?

Mutations occur at random throughout the genome. Most mutations will be neutral. That is, they are neither bad or good from an evolutionary viewpoint. The mutations are neutral because the genome for most organisms is non-functional. Mutations that occur in the functional regions of DNA (i.e., protein-encoding and related regions) are more likely to be detrimental (bad) because the mutation may negatively affect the function of the protein or even the ability to produce the protein.  However, some mutations are beneficial. The mutation may actually enhance the functionality of the protein or even produce new proteins.
A couple of factors have to be considered regarding mutations.  The mutation rate is very low.  For example, Kumar and Subramanian (2002) compared the DNA sequences of 5669 protein-encoding genes from 326 species of mammals.  Their results suggested that the average mutation rate among mammals is 2.2 x 10$^{-9}$ per base pair (bp) per year.  This means that, on average, a point mutation has changed each DNA nucleotide position in the mammalian genome slightly more than twice (2.2 times) every billion (10$^9$) years. That's a lot of time!
However, this same rate occurs in every individual in the population, so you have to consider the population sizes of the organisms. So, let's do a simple exercise. Consider a species like the rock pocket mouse or another small mammal that has a very short generation time. For this simple example, let's assume the generation time is one year. That means that the mutation rate of 2.2 x 10$^{-9}$ per bp per year would then correspond to 2.2 x 10$^{-9}$ mutations per bp per generation. Generation time is important because new mutations are inherited only through reproduction.
Assume the average mammalian diploid genome is about 6 billion (6 x 10$^9$) nucleotides in size. The number of heritable mutations that occur in a single offspring is
$$(6 \times 10^9) \times (2.2 \times 10^{-9}) = 13.2.$$
Next, assume that about 2.5% of the mammalian genome is composed of functional, transcribed sequences that may affect the phenotype (the traits of the organism). That means that, of all the mutations that occur in every offspring every generation, about 2.5% could potentially affect the phenotype.  That is,
$$13.2 \times 0.025 = 0.33.$$
Still a small number.  But, now we have to account for population size. Small mammals, like mice and voles, generally have large population sizes.  Assume that the population of rock pocket mice contains 100,000 reproducing individuals. If so, then
$$0.33 \times 100,000 = 33,000,$$
which is the number of new heritable mutations that could occur in the population. Most of these mutations will be detrimental and removed from the population by natural selection but, if even a small fraction of these new mutations are beneficial, then natural selection can cause these beneficial mutations to increase rapidly in frequency in the population during future generations.
In humans, Nachman and Crowell (2000) estimated that the average mutation rate was 2.5 x 10$^{-8}$ mutations per bp per generation (not year), by comparing the genomes of humans and chimps. If we assume the same genome size and effective human population size of 500,000 individuals, then applying the same math suggests that 1,875,000 new mutations that potentially affect phenotype occur in the human population every generation. Again, only some of these will be beneficial but that is still the possibility of a number of new beneficial mutations. In evolutionary terms, a mouse or human generation is the blink of an eye.
How long would it take for a beneficial mutation to spread through a population? That depends on two things. How beneficial is the mutation (called the strength of selection, s) and the population size? To estimate how long it would take for a beneficial mutation to spread through a population, we can use the formula,
$$t = \frac{2}{s}\mathrm{ln}(2N_e),$$
where $t$ is time in generations, $s$ is the strength of selection, and $N_e$ is the effective population size (number of reproducing individuals). For the strength of selection, let's assume $s=0.01$, which is weak but positive natural selection. Going back to our rock pocket mice with $N_e = 100,000$, then the beneficial mutation would be spread throughout the population in only 2441 generations (remember, we're talking evolutionary time so 2000 years is nothing). If $N_e = 10,000$, the mutation spreads in only 1981 generations.  If we increase the strength of selection t 0.2, then the times are 122 and 99 years for population sizes of 100,000 and 10,000 years, respectively.
These "back of the napkin" calculations show just how quickly even weakly beneficial mutations can appear and spread throughout a population. Yet, this doesn't include other types of mutations like gene duplications that can also allow new proteins to evolve. For example, human ability to see red colors is due to a simple gene duplication (Nathans et al. 1996 and references therein). This duplication also explains the common form of red-green colorblindness.
Whew!
There's yet more to our mutational story. Consider humans and chimps, which are nearly identical from a genetic standpoint (between 96-99% depending on how you calculate it) yet they appear very different.  If humans and chimps diverged from their common ancestor within the past five million years, how could they differ so much? This question was initially posted by [King and Wilson (1975)]. They argued that mutations to structural proteins (like those that compose bones and muscles) would not be enough to explain the phenotype differences between humans and chimps. The proposed that regulatory genes are the key to understanding the big differences. Regulatory genes are those that control other genes, by turning them on or off and other important functions. Changes to the regulatory genes can cause fairly rapid changes to the phenotype.
This understanding has led to the broad (and fascinating) field of evolutionary developmental biology. This field focuses on how mutations in regulatory genes associated with development (from embryo to adult) have had a long-term evolutionary impact. The field is rich with examples, but one cool one is associated with duck feet and bat wings. Let's begin with the embryo. Most vertebrate embryos have membranes between the digits (fingers and toes) during an early stage of development. For most vertebrates, the membranes are lost later in development. The small flaps of skin you have between your fingers are the remnants of your embryonic membranes.
A set of regulatory genes called BMPs (and a couple of others) are responsible for causing the loss of the membrane in vertebrates. However, through different sets of mutations, the BMPs are not able to function in duck feet and bat hands. Thus, they both end up with membranes between their digits (Weatherbee et al. 2006).  Thus, two different mutations block the same set of developmental genes, leading to novel adaptations in two very different types of vertebrates. One final example is the evolution of bird feathers from scales. As you may know, birds are evolved from dinosaurs. It turns out that bird feathers and alligator scales (alligators are birds closest living relative) use the same regulatory genes to develop. The genes are BMP2 and SHH (sonic hedgehog for fans of the old computer game) (Harris et al. 2002). Other regulatory genes underlie the different types of feathers, like downy feathers and flight feathers (Harris et al. 2002).
Literature Cited
Harris, M.P. et al. 2002. Shh-Bmp2 Signaling module and the evolutionary origin and diversification of feathers. Journal of Experimental Biology 294: 160-178.
King, M.-C. and A.C. Wilson. 1975. Evolution at two levels in humans and chimpanzees. Science 188: 107-116.
Kumar, S. and S. Subramanian. 2002. Mutation rates in mammalian genomes. Proceedings of the National Academy of Sciences USA 99: 803-808.
Nachman, M.W. and S.L. Crowell. 2000. Estimate fo the mutation rate per nucleotide in humans. Genetics 156: 297-304.
Weatherbee, S.D. et al. 2006. Interdigital webbing retention in bat wings illustrates genetic changes underlying amniote limb diversification. Proceedings of the National Academy of Sciences USA 103: 15103-15107,

I've asked many (hundreds of) questions on stack exchange, and time and time again, people have raised the bar, amazing me at how far they were willing to go to teach me every aspect of a question that I had asked. This one just took the lead. Thank you for your time.

@jt0dd You're welcome. I'm glad you found the answer helpful.

"Traits evolve through the biological processes of random mutation and natural selection."
Could you show us some evidences for this claim?

About your question
This kind of very basic question has the drawback to need a very long answer. In consequence, your question might get some close vote. I'll do my best to help but you might want to look at some source of information as an introduction to evolutionary biology. A book eventually or Khan academy maybe.
Darwin's evolution theory
The expression "Darwinian evolution theory" easily yield to misunderstanding because Darwin was probably the most important scientist (and one of the first if not the first) to develop evolution theory but not the only one. Evolution theory is not anymore Darwin's evolution theory.
What is Natural Selection? Lewontin Recipe
You list:
- Survival of the fittest
- Random mutation
- Natural Selection

It is a list of different concepts that might be present in evolutionary biology but its nothing like a recipe for evolution to occur. This list I think already shows some point you misunderstood about evolution. The Lewontin recipe is a good way in order to understand what is natural selection and when it occurs. The Lewontin recipe says that natural selection occurs whenever:

Individuals in a population vary in terms of a given trait
This trait has some (additive) heritability. Here is one of the several posts that explain the concept of heritability. It might be slightly a post that is a bit advanced for you though but shortly speaking it means that offspring are more similar to their parents more than they are to other non-kin individuals in the population.
The fitness varies (not necessarily linearly) as the trait varies.

Simple example:

In a population, there are blue pens and red pens
Reproduction is asexual and blue pens create other blue pens while red pens create other red pens.
blue pens make more offspring than red pens.

In such a situation, natural selection occurs yielding the frequency of the blue pens to increase in the population while the frequency of red pens will decrease.
What is evolution?
Evolution is not only natural selection. It is for example very important to consider random events. One of them is mutation, another is genetic drift (I am not trying to list every parameter that influence evolution but only to give you a sense of why natural selection is different than evolution with a goal of explaining why a trait that is needed do not necessarily appear). Both mutations and genetic drift explain why a species will not necessarily be perfectly adapted to its environment.
Mutations
In the broad sense mutation is any change in the DNA sequence. Some changes are more likely to happen than other but in any case, the likeliness of these changes to happen is not dependent on the consequence they will have on the phenotype (shortly speaking, a phenotype is how an individual looks like) and on the reproductive success. So mutations occur randomly and the specific mutation that would be needed in the population may not occur. Therefore saying, if a trait is needed (in the sense of "if a trait would be beneficial"), then a mutation will occur to make this trait existing is totally wrong. You may be surprised by the level of adaptation of life but this does not mean that what they needed was created with the purpose to help these individuals surviving but it only means that random mutations occur, most of them are deleterious (decrease the reproductive success) while few of them are beneficial (increase the reproductive success) and those that are beneficial are more likely to rise in frequency in the population.
Genetic drift
If the change in frequency of mutations would depend exclusively on natural selection, then I would not have said before that a beneficial mutation is more likely to raise in frequency but I would have said that a beneficial mutation will raise in frequency. An intuitive explanation of what is genetic drift can be found on this post. It will also allow you to understand why a small population undergo a more random change in frequency of their genes that are big population.
Therefore, when you say that you noticed that Any time a species has needed the development of a specific feature to survive, it has developed that feature, and that feature precisely is wrong. You only noticed that species has some level of adaptiveness if I can say so. It is very hard to imagine what new mutation would be beneficial of a given individual in a population but there are in reality many mutations that are beneficial that has never occurred or that has disappeared because of genetic drift. Also, as it is implied in the Lewtontin recipe different individuals have different traits yielding to different reproductive success. If you do not consider mutations that have never occurred but only to sites in the genome that are polymorphic (where different variants exist in the population), then it is worth knowing that any single individual carries quite a lot of deleterious variants. These deleterious mutations explain many genetic diseases. No, we are not perfect.
About your question again
Hope that helps a bit. But I would need days in order to explain further what evolution is. It is a bit field in biology. Your question is a bit too broad and as I said at the beginning you should seek some information by yourself and come back to this site with a question that can be more quickly answered.
Hope that helps!

Taking out of its context the statement mutations occur randomly makes little sense. What I meant above is that the probability of that a given mutation has a particular effect is independent from the need of the lineage or if you prefer independent from what will cause a higher fitness for the carrier. If you can clarify what exactly you want evidence for, please just open a new post and ask your question.

To be accurate I did not say in my above comments that mutations occur independently from environmental changes because the sentence mutations occur independently is unclear. Typically, the mutation rate might be affected (adaptively and not adaptively) by environmental changes. If you are able to ask an accurate question, then please just do so in another post.

Here are two references (among many others). Mutation rate is affected adaptively by stressors (Stress-induced mutagenesis in bacteria. Note that most examples I have heard of so far concern increase in mutation rate in plants as a bet-hedging strategy) and radioactivity (one type of environmental change) affects the mutation rate (Radiation-induced mutation rate).

You will be banned because you fail to follow the rules. Asking tons of follow-up (and eventually unclear) questions in the comments is also not following the rules. I will not answer further questions in the comments unless your comments are more on-topic.

I am sorry but IMO, you are extremely opinion-based, know little to nothing to evolutionary biology and yet think you can disprove some of its statements. Please just take an introductory course to evolutionary biology (as I already suggested a number of times) and stop harassing us with your unclear and never ending comments. I am flagging your last comment (although I would have preferred flagging some other comments of your that are have now been deleted). Sorry and good luck in your seek for knowledge.

Comments are not for asking questions that were not within the scope of the original question. Just open a new post. And as a general advice (that I already gave you a few times), you should try to understand what evolutionary biology is about before trying to disprove it. Just take an introductory class to evolutionary biology.

"Comments are not for asking questions that were not within the scope of the original question."
I'm asking about your answer to the question.
I think it's pretty legit to do so as long as it makes sense(which I believe is the case).

To the moderator, why did you delete my penultimate comment?

Short answer version:

It seems plausible to me that we (advanced life) could have a
  biological mechanism to "write" needed alterations into either our own
  DNA or our reproductive DNA over time, triggering the very specific
  evolutionary developments necessary to our survival without relying on
  random mutation.

No, it's not.  Despite what your feelings tell you, despite what you wish the case might be, there is no evidence in molecular biology to suggest that such a mechanism exists, there is no evidence that such a mechanism is required to explain the different phenotypes we see.

That does answer my question in the most direct way, however I'll give the correct answer to the one which shows extreme effort and detail, with excellent explanations. Thank you for this, nonetheless.

I agree that the longer answers are more detailed and more useful, but one has to admit that it is hard to give a detailed description of a mechanism that does not exist.

I was not criticizing this answer, only explaining that I thought the more detailed one was more deserving of the reward. However, +1.

Any time a species has needed the development of a specific feature to survive, it has developed that feature, and that feature precisely.

This statement is clearly false. The dinosaurs didn't develop what they needed, did they?
It turned out that on this occasion, the mammals happened to be best adapted to the conditions at the time, just as the fish had managed to get the upper hand over the large arthropods and the ammonites previously.
In hindsight many of nature's solutions seem wonderfully elegant, but they were arrived at by luck under intense pressure to survive. The fact that our eye is designed with blood vessels on the front of the optical surface instead of the back is an example of a design that could have been done better if thought out from scratch. There are many vestigial features from previous generations which persist, even though they are no longer needed. Notice that flatfish hatch with eyes on opposite sides of their head and one eye then migrates to be on the same side as the other, and whale embryos that have teeth which have disappeared by the time they are born, etc.
Natural selection is a combination of lucky mutations which happen to fit in with the prevailing conditions. It's a tough world out there. Even the plants are strangling each other, as can be seen on this video: https://www.youtube.com/watch?v=aNjR4rVA8to
The turtle didn't have much time to stare longingly at the leaves he couldn't reach. Some other turtle with a slightly longer neck came and ate them. And he got bigger and stronger and fought with the first turtle so he got to mate with all the females. And so the next generation of turtles had longer necks than the last.
It's easy to forget, with our comfortable lives, what a struggle nature is. The reason for this is that humans as a species have developed the most devastating weapon of all: cooperation. Compared to most other organisms, we treat other individuals of the same species pretty well (most of the time) and we actually teach each other how to do things. While some other species cooperate among individuals, humans have taken this to a whole new level. As a result, we have been able to eradicate many species which pose a threat to us and bring many other species which are useful to us under control.
If you want to know why this didn`t happen before: humans evolved from an ape-like creature that, due to changes in its environment, came down out of the trees and started walking on the ground. This creature then had its hands free to use tools, and by sheer chance this combination of factors made a bigger brain advantageous, so this creature (which was already social, like apes but unlike octopi, one of the few other creatures blessed with the ability to perform complex manipulations) became even more intelligent and began to educate its offspring in how to control its environment.
There is nothing in biology which enables the mutation of genes to be directed. Finally, human technology has developed to the point where it may be possible to modify genes directly. However, there are significant ethical issues regarding the use of this technology. The termination of an "imperfect" human is frowned upon because it is considered that all members of the species should be given the best chance to survive. Besides, it is not at all clear if there is really ever such thing as a "defective" gene. For example carriers of the gene responsible for sickle cell anaemia have increased resistance to malaria.
Anyway, long before humans were able to manipulate genes directly, they were able to produce massive changes in the phenotype of dogs in a remarkably small number of generations. There is a breed of dog adapted to every possible use. An unfortunate consequence is that the gene pool in each breed is rather small, leading to breed-specific illnesses. If these breeds were left alone it would take many generations for mutations to allow their genotypes to diversify again. And who knows what the final animal would look like?

It seems plausible to me that we (advanced life) could have a biological mechanism to "write" needed alterations into either our own DNA or our reproductive DNA over time, triggering the very specific evolutionary developments necessary to our survival without relying on random mutation.

There is no evidence for such a mechanism, and it is very unclear how a mutation could be proved beneficial without being tested in the environment. What there is, is a way of mixing and matching genes, so that the best ones can propagate throughout the population. Unicellular organisms do this by a variety of means. For multicellular organisms the way of doing is sexual reproduction.
The cost of this is enormous. Look at a flowering plant. That flower has evolved exclusively to enable pollination, typically by insects. In some cases, virtually all the plant's energy goes into making that flower and relatively little into making the actual seeds. Plants do have a particular problem exchanging genes because they do not move about. Stationary animals, such as the barnacle, also have similar problems. The barnacle solves this by having a "penis" several times longer than its body length so that it can copulate with its neighbour without moving from its spot. In humans, fully half the population is male and therefore unable to bear offspring.
Asexual reproduction is far more efficient at producing offspring but does not enable the interchange of genes. The offspring are clones of their parent and therefore have the same genetic strengths and weaknesses. Asexual reproduction does exist, even in some animals, but exclusively asexual reproduction would preclude the spread of beneficial mutations. That's why organisms invest so much energy in sex.
Aphids are a good example of an animal that reproduces both sexually and asexually. At the boom times of the year, aphids reproduce asexually and are actually born as already pregnant females! When the availability of food slows down, they switch to the slower, sexual reproduction system with males and females.
In many animals, males must demonstrate their good health in order to be able to mate with the females (who are choosy, because they have to take the cost of bearing the young.) In many large herbivorous mammals, this is done by males fighting. Male birds often display their health by elaborate plumage, the classic example being the peacock. It is debatable whether such a conspicuous waste of resources is really beneficial to the species, but the females have evolved to select males in this way. In some fish, there is only one male in a group, and when something happens to him, the biggest healthiest female actually changes sex to become a male.
So, if an organism were able to program its own genes, why invest so much energy in sexual reproduction?

In answer to the final question, the answer is because it feels good. :)

@MikeTaylor indeed, even now that we can make babies in a test tube, I can't see the old way going out of fashion.

"I imagine that turtle looking up at that food, and sub-consciously
  wishing to get to it, constantly straining, for its entire lifetime.
It seems plausible to me that we (advanced life) could have a
  biological mechanism to "write" needed alterations into either our own
  DNA or our reproductive DNA over time, triggering the very specific
  evolutionary developments necessary to our survival without relying on
  random mutation."

That is a pre-Darwin idea of evolution called "inheritance of acquired characteristics" or Lamarckism after it's creator French natural philosopher Jean-Baptiste Lamarck. Lamarck postulated that given the use of tissues altered those tissues e.g. lifting weights makes muscles bigger, then an organisms descendants would benefit if everything the parent's tissues "learned" could be passed on.
There are actually epigenetic factors in cells that selectively turn genes on or off or otherwise modify their use generation to generation. But this is not evolution because the genes are always there, ready to be used if needed and no new information is ever created.
The flaws in Lamarckism are that, even if the mechanism existed to transmit acquired characteristics, how would it know what characteristics led to what outcome? How could it distinguish positive changes from negative ones?
Most fatally, how could an organism evolve a system that was not related to an existing behavior? For the turtle to stretch its neck, it must desire to eat the leaves and exert effort to do so. How did it acquire the behavior of desiring to eat the leave in the first place? Going forward, if the plants it does eat goes away, how would it ever find another food source? It wouldn't desire to eat inedible plants so it would never exert itself to do so and would never pass that exertion on to it's young.
The hiccup in your understanding of Darwinism is that you've got it backwards. Species don't find solutions and evolve. It's not something species do. It's something that happens to species, a force from the outside. It's not analogous to humans setting down to consciously solve a problem.
Darwin was originally going to use the analogy of "wedging" instead of "natural selection." He wanted to emphasize that it was the environment squeezing in on species that formed them. (Today we think of wedges largely for their splitting power but in but in Darwin's day, if you wanted to compress something you used a wedge hammered in from the side. It was a common tool that performed the same jobs as jacks and hydraulics do today.) But he went with the anthropomorphic analogy of nature being an animal breeder selecting for traits for reproductive success and a lot of misunderstandings followed.
Evolution is not random. Only variations themselves are random. The selection of them is not. It's like shooting dice. The fall of the dice is random but only certain values of dice are winning number and are "selected." The same mutation might show up in every generation for millions of years but produce no change until the environment changes to make the mutation useful.
Species have no existence independent from their environment. The environment squeezes them into a specific form, one that best satisfies the demands of the Second Law of thermodynamics. If the environment doesn't change, then the organism won't either. From that perspective, adaptation is about as amazing as a rock rolling downhill. (That would look pretty fantastic if you didn't know about gravity.)
Imagine you had never seen clay and never seen molding. Your walk along a stream bank lined with clay. Walking one way you pass a blank stretch of clay. After you pass, a leaf falls into the claw and creates a near perfect imprint before being blown away. When you return past that spot, it looks like the clay has somehow altered itself, against all probability, into an exact mirror duplicate of a leaf. How you might wonder, could the clay possibly know how to exactly duplicate the shape of a leaf?
But the clay did nothing. The clay did not alter to fit the leaf, the force of the falling leaf altered the clay.
Likewise, species do not evolve themselves, they are evolved by external forces. Species seem to miraculous fit their ecological niches but, just like the clay, did nothing to shape themselves to the niche. Just as the clay will be passively shaped by the pressure of molding, species have no choice but to assume the forms they do.
It's not survival of the fittist but survival of the fitted.

The answer provided by Mike Taylor is just perfect and complete.
However, I'd like to add some thoughts of my own in a more colloquial style:

Survival of the fittest is not always true. There is also "survival of the luckiest" (e.g. the fittest is showing off in the beach with the other turtles and is struck by lightning).
Reproduction is not that simple and many times the female mates with several mates (apart from the fittest one) and a paternal test should be procured.
Mutation changes are not always gradual (i.e. the turtles might develop a long neck in just one generation).
Mutations don't always lead to a phenotype change. Sometimes, depending of the environment, the phenotype change doesn't occur. For example, the turtles might only grow a long neck if the live in a sunny island.
Not all mutations are beneficial and not all beneficial mutations have an impact on survival (e.g. many actors/actresses are not very tall although they reproduce successfully).

In my opinion there are many shades of grays in between the ideas behind evolution.
The features of the "fittest" are sometimes lost by random reasons as the listed above, and the features of the "less fitted" are sometimes transmitted.
And finally, sometimes, an organism develops (or is developing) a mechanism to alter the genes directly (e.g. human beings). Where would that lead? Does evolution mean something anymore?

To add to the previous answers that treat specifically of the biological Darwinism, there is also Universal Darwinism which postulates that evolution is a natural phenomenon that appears when a set of conditions and constraints are present. And indeed, it has successfully been applied to a number of fields (see below the quote), which seems to imply that evolution is not a property of the evolving individuals (as you implied) but a property of the system where the individuals evolve (as long as the individuals satisfy a few special properties, namely variation and heredity, see below).
Here's the definition from Wikipedia:

At the most fundamental level, Charles Darwin's theory of evolution states that organisms evolve and adapt to their environment by an iterative process. This process can be conceived as an evolutionary algorithm that searches the space of possible forms (the fitness landscape) for the ones that are best adapted. The process has three components:

variation of a given form or template. This is usually (but not necessarily) considered to be blind or random, and happens typically by mutation or recombination.
selection of the fittest variants, i.e. those that are best suited to survive and reproduce in their given environment. The unfit variants are eliminated.
heredity or retention, meaning that the features of the fit variants are retained and passed on, e.g. in offspring.

After those fit variants are retained, they can again undergo variation, either directly or in their offspring, starting a new round of the iteration. The overall mechanism is similar to the problem-solving procedures of trial-and-error or generate-and-test: evolution can be seen as searching for the best solution for the problem of how to survive and reproduce by generating new trials, testing how well they perform, eliminating the failures, and retaining the successes.
The generalization made in "universal" Darwinism is to replace "organism" by any recognizable pattern, phenomenon, or system. The first requirement is that the pattern can "survive" (maintain, be retained) long enough or "reproduce" (replicate, be copied) sufficiently frequently so as not to disappear immediately. This is the heredity component: the information in the pattern must be retained or passed on. The second requirement is that during survival and reproduction variation (small changes in the pattern) can occur. The final requirement is that there is a selective "preference" so that certain variants tend to survive or reproduce "better" than others. If these conditions are met, then, by the logic of natural selection, the pattern will evolve towards more adapted forms.
Examples of patterns that have been postulated to undergo variation and selection, and thus adaptation, are genes, ideas (memes), neurons and their connections, words, computer programs, firms, antibodies, institutions, quantum states and even whole universes.

Also, you may be interested in some terminology associated with this theory, for example for John Maynard Smith an individual that can evolve in an evolvable system is called a Unit of evolution [1]. This shows how much abstract and generalizable evolution can be.
[1]: Fernando C, Vasas V, Szathmáry E, Husbands P (2011) Evolvable Neuronal Paths: A Novel Basis for Information and Search in the Brain. PLoS ONE 6(8): e23534. doi: 10.1371/journal.pone.0023534

There are indeed massive evolutionary control systems integrated into DNA. They constitute the major force for efficient change in living beings.
Random DNA mutations are not as beneficial as controlled ones, you can see random single gene mutations at work in medical books: Anemia, cancer, cheese smelling sweat, no sweat glands, skin conditions, scales, brittle bones, lactose tolerance, These are all examples of mutations of single proteins and single growth hormones and so on.
Instead of random DNA mutations, life-forms control their rate of change and types of variations in very efficient ways, changes in color, longer and shorter bones/arms/legs which you can see in humans, physical maturation times, length and quantity of hair, all these things are safe for an animal to have lots of genetic variation with. Changes in bone length vary more than 10 percent in a single generation of humans, but changes like lactose tolerance occur only every 100ds of generations. Therefore there are hundreds of genes for controlling growth hormones as it's selection-important. If color changes become important to an animal, for example, birds, fish, and butterflies, then hundreds of genes are devoted to color. If color is not important, for example, northern and snow animals, then few gene changes are devoted to color, The many Color genes of a tropical animal would go dormant very fast if it were exposed to snowy conditions.
It makes sense for DNA to favor developments that encourage reproduction and survival in variable settings, and indeed DNA is supercharged to deliver mostly useful morphological and chemical changes in large numbers. Plants, conversely, need to change their chemicals alot to attract and repel animals, whereas animals do not need to attract other animals for food, only to defend themselves, that one reason why animals have a lot less chemical variety than plants. Only Chinese use animals for medicine, and there are few aspirins and sedatives derived from animals. Animals cannot produce powerful random chemicals because their nervous system hormones and cell walls are less robust than cellulose cells and plant hormones. Otherwise, animals would have more variable smell and taste, but all mammals taste similar.
It's the same with computer evolution. If you tell a computer program to vary DNA randomly or to create life-forms randomly, it will have epileptic, disorganised animals that flop around, roll around, hit walls, and that is not what animals do to evolve. If you equip a computer evolution program with DNA tool kits copied from nature, you will much faster have meaningful animals... i.e. simple locomotive insects. If you tell the computer to use sinusoidal limb movements like fish fins, millipede legs, insect legs, using nerve impulses, and to create metameric life forms, you will have alot more success than just adding limbs onto random parts of the body, using random pattern nerve impulses and so on.
It's not an easy thing to study, as it is very complex. I would love some statistics and journals regarding types of evolutionary changes that are prevalent in different life-forms.

Can you please add some references to your answer?

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

authors: Bob Jarvis - Слава Україні


text:
Parameters of Variant calling analysis
What is the good or stringent parameter for variant calling?
At present using the DP > 10 and Q > 30 for Variant calling. Is it ok?

What tool are you using and what are you calling on, whole genome, exome?

@CMosychuk, its Whole genome sequencing

We will be needing some additional information to answer your question more completely:
What sequencing platform are you using? Illumina HiSeq/MySeq; Ion proton
What type of sequencing (as noted by @CMosychuk): Exome or Whole Genome?
What type of variant caller (as noted by @CMosychuk): Unified Genotyper; Haplotype Caller; TVC
The QUAL metric is heavily dictated my sequencing depth, so if you use 30 (phred-scaled), that would be an accuracy of 99.9%.
The typical QUAL metric used by most sequencing studies is 20 so using 30 may cause accumulation of false negatives. But again, depends on the type of sequencing and platform used.

this looks more like a comment than an answer - once you have earned some more reputation points you will be able to comment anywhere, but until then please refrain from commenting as an "answer" - thanks for your contribution!

@VanceLAlbaugh I won't classify this as a comment outright, the latter parts of the answer are in fact answers to the question.

@MarchHo I'll take your word for it - not obvious to me (an outsider in that specific field)

Its whole genome sequencing, Illumina HiSeq 1000 platform, Type of cariant caller is Unified genotyper. Tools using samtool, vcftool.

For variant filter using SNPeff

Try sticking with a QUAL of 20. Illumina usually produces well-mapped reads. If you think some of the lower quality variants are artifacts, try sanger sequencing them and see if they validate. A QUAL of 30 seems high for Illumina data.


text:
The biophysics of the protection of the brain by cerebrospinal fluid
The two mechanisms I've seen mentioned are the cerebrospinal fluid (CSF) acting as a hydraulic cushion or shock absorber, and CSF creating a micro-gravity environment through buoyancy.
I have very little understanding of the former, but I do have a vague idea about the latter: because the brain is submerged in a fluid (the densities of the brain and CSF are also similar I think), it experiences a buoyant force upwards that counteracts the force of gravity on the brain, hence decreasing its "effective weight" from around 1400g to about 50g.
How does this help precisely? The explanation I've seen that I could understand is that it makes it so that the brain isn't pressed up against the base of the skull due to gravity, and so that it doesn't get deformed under its own weight. This buoyancy also helps the various structures attached to the brain, like nerve roots and blood vessels, hold it up and support it. Wikipedia also says that it allows the brain to maintain its density without being impaired by its own weight, which would cut off blood supply and kill neurons in the lower sections without CSF. This explanation is plausible but I'm not sure if it's the entire story.
There's also this bit from "Neuroscience in Medicine" that says the decrease in effective weight decreases injury by reducing brain momentum in response to stresses/strains inflicted on the head. How does that work? I'm not super familiar with the physics of buoyancy, I just know the basics. I don't understand how it reduces momentum during movement.
I couldn't find anything that went into the physics of the whole hydraulic cushion thing, and I’d appreciate an explanation.

This is a cool question! Here's another way to understand the "momentum" part: A function of CSF that comes from its physical properties as fluid is to protect the brain from the damage that would result from a sudden movement of the skull. Any rapid acceleration/deceleration of the head has the potential to injure the delicate contents contained within.
The CSF helps reduce the potential damage in such an event by acting as a cushion and a shock absorber.(https://www.ncbi.nlm.nih.gov/books/NBK470578/)

@Bipasha thanks! So essentially, “reducing momentum” is more or less the just saying the same thing as “it acts as a hydraulic cushion”. That makes things simpler.

In terms of buoyancy, you are correct in your understanding that CSF creates a micro-gravity environment around the brain. This buoyant force essentially counteracts the downward pull of gravity on the brain, reducing its effective weight as you described. This decrease in effective weight plays a crucial role in maintaining proper positioning and preventing deformation of neural structures within the skull. As for how CSF acts as a hydraulic cushion specifically, think of it as providing support and distributing pressure evenly throughout different regions surrounding the brain and spinal cord. The fluid-filled spaces allow for dynamic adjustments in response to changes such as changes in posture or intracranial pressure fluctuations.
1. CSF compression: When the brain is subjected to a sudden force, the CSF is compressed, which increases its pressure.
2. Pressure transmission: The increased pressure is transmitted through the CSF to the surrounding skull and meninges (the protective membranes covering the brain).
3. Force distribution: The pressure is then distributed evenly throughout the skull and meninges, reducing the force applied to any single point on the brain.
4. Shock absorption: The CSF acts as a shock absorber, reducing the amplitude of the force transmitted to the brain.


text:
What's the cause of the scars on these cherries?
These cherries have some scars. Are they coming from a disease? Is it correct to call them "Cherry scabs"?
Here's the photo:  -

U think those happened way before the cherrie were ripened, else the lack of acid would have made them rot from exposure, so I don't know why they would split at that stage, considering they usually split from excess rain.


text:
Is nucleoside-triphosphate delivery to RNA or DNA polymerase active or passive?
Are nucleoside triphosphates (NTPs) actively delivered to RNA polymerase (similarly dNTPs to DNA polymerase) through some active chaperoned process, or are they so abundant in the nucleus that they rely simply on stochastic diffusion?
Are there any relevant papers on this process?

You or someone else seems to have changed the question from dNTPs and DNA polymerase to NTPs and RNA polymerase. This negates the answer that @BlueFoxy went to the trouble of providing. In any case I'm still not clear what you are asking. Are you asking about how the precursors get from the cytoplasm, where they are thought to be synthesized, to the nucleus, or to the polymerase when already in the nucleus? If the later, why do you think the situation is any different from any other stochastic process involving enzymes and substrates?

The principles would be the same for NTP-RNAP and dNTP-DNAP so it doesn't really matter.

@WYSIWYG — Not necessarily, although the whole idea of chaperones for (d)NTPs seems absurd to me. I've changed the title slightly as I see the question has been edited to include this.

There have been significant edits to my question by moderators or others, and I'm not sure I understand the wording of my own question anymore. My question is literally just the colloquial "is there something in the nucleus actively delivering nucleic bases to polymerase to attach to new DNA strands, or does it just happen through random collisions/diffusion)

@MikeFlynn We just made the statement more scientifically accurate. Don't worry; we have not changed the meaning. If left to what it was, your question would have been considered unclear.

@Mike Flynn Delivering NTPs to be used by a polymerase expends energy from ATP ... therefore it is active transport. :)  (While that seems like an abuse of the definition, I'm not sure it is!)

The amount of dNTPs is so important and sensitive the level of dNTPs should be optimum  not lower or higher. Lower amounts lead to insufficiency  and higher amounts lead to increased mutation rates. Also, this optimum amount of dNTPs should last for a couple of minutes to supply dNTPs needed for replication. The delivery of dNTPs is due to molecular signalling & stochastic diffusion.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2847218/
"Eukaryotic cells contain a delicate balance of minute amounts of the four deoxyribonucleoside triphosphates (dNTPs), sufficient only for a few minutes of DNA replication. Both a deficiency and a surplus of a single dNTP may result in increased mutation rates"

http://onlinelibrary.wiley.com/doi/10.1111/j.1349-7006.2010.01719.x/pdf
"Optimization of intracellular concentrations of dNTPs is critical for
the fidelity of DNA synthesis during DNA replication and repair
because levels that are too high or too low can easily lead to
increased rates of mutagenesis"

http://www.nature.com/ncb/journal/v14/n7/full/ncb2540.html
"Production of deoxyribonucleotide triphosphates (dNTPs) is essential for DNA synthesis during replication and repair, and abnormal or imbalanced dNTP levels increases mutation frequency. Pagano and colleagues now demonstrate that the SCF-cyclin F ubiquitin ligase controls dNTP production during the cell cycle and following genotoxic stress"

http://www.ncbi.nlm.nih.gov/pubmed/22234185
"alterations in dNTP pools are associated with increased mutagenesis, genomic instability and tumourigenesis"

To be clear, are you saying that nucleosides can arrive both by chaperones and diffusion?

@James chaperons have nothing to do with dNTPs delivery at least not directly . http://faculty.washington.edu/baneyx/Chaperones/Chaperones.html chaperons just control the folding and unfolding process of proteins by interacting with mediators .

You provide some good references on the regulation of dNTP synthesis, but you do NOT answer the question. I would up-vote your answer if you added a conclusion on the lines of "In none of these papers is there any suggestion that the dNTPs enter the nucleus and reach the DNA polymerase by any other mechanism than diffusion. Furthermore, with rare exceptions (e.g. exotic metal cofactors), chaperones are only involved in the delivery of proteins. In the absence of any published evidence it is reasonable to conclude chaperones are not involved."

Many processes in the cell, also processes involving compounds that have a lower abundance than the NTPs, rely on stochastic diffusion. Even the polymerase is not actively transported to the nucleic acid, it just diffuses until it finds a proper binding place.
Also, the energetics of active transport would not make sense. One of the NTPs is ATP, one of the major energy carriers in the cell. It would make little sense for the cell to actively transport ATP to the polymerase on the nucleic acid, because active transport needs energy, thus likely ATP or something similar itself. This would then have to diffuse to the transporter to keep it moving. It would be cheaper for the cell to just use that ATP directly, because you're relying on diffusion in both cases.
This is not even taking into account that 1 protein cannot actively move across the cell, even expending energy. Systems that do something like this are much more complex, such as myosin (moving along actin filaments).

One of the dNTPs is certainly NOT ATP, it is dATP. And chaperones do not necessarily require energy. I'm afraid it's your arguments that don't make sense, irrespective of the validity of your conclusion.

Chaperones aren't diffusing any faster without energy, and sorry for automatically typing dNTPs (although you could have just corrected this).

As regards dNTP and NTP, I think the question has been changed from one  originally about DNA and I didn't notice. I assume we are talking of chaperone proteins. I know of no chaperone proteins (or indeed any other protein) which uses the energy from hydrolysis of ATP to increase its diffusion in solution (rather than across a membrane, which is not relevant to the question). Do you? And what do you mean by 'active transport' needing energy? Are you thinking about active cation transport, which is irrelevant here?

Diffusion is free, if you want to actively create a concentration gradient (higher at one point than another) it's going to cost energy, no matter how you do it.

I know diffusion is free, but you seemed to be suggesting you could use "energy" to accelerate it. But who wants to create a concentration gradient? If the NTPs diffuse to the polymerase they will be removed by reaction, pulling more into the nucleus by mass action.

That's why chaperones are not used here, I'll try to clarify.

I know chaperones aren't used here. I was criticizing the arguments in your answer, not your conclusion. The only examples of chaperones for small molecules I know are for things like Nickel in urease. Otherwise, they are only used for proteins.


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Worm compost cannot have cooked food
I live in the Netherlands and it is getting fashionable to compost with worms. After investigating a few websites I noticed that most websites suggested that I cannot feed the worms leftovers from citrus fruits. This seems logical. I then started noticing that people advise against feeding the worms cooked food.
I'm no biologist but I cannot imagine a reason why cooked food is bad for the worms. Could anybody explain why this might be in layman’s terms?

If you can, please add some references to this claim (as I am a biologist and can't imagine a reason either).

The only thing I can think of is that cooked foods often have added fat which might attract animals or that cooked foods tend to compress and don't allow for aeration but neither of these seem particularly concerning if there's a good mix of other things in the compost as well

I've been putting cooked food in my small domestic worm farm for years.  It works ok and the worms seem happy enough but downsides are that it can get a bit smelly in warmer weather and attracts flies.  My suspicion is that fly larvae and other small organisms on the top layer end up breaking down anything the worms can't handle.  The meat content in the cooked food would tend to be very low, primarily veg and carbs.  Also very little processed food goes in.  Final compost is excellent feeding for rhubarb, fruit and veg.

I think that "compost with worms" sounds like a mix of composting and worm farms. The two environments are a bit different: Worm farms are a fine culture using agriculture/garden waste of leaves and natural garden detritus, and compost can be more messy and contain food, cardboard, paper, waxy hay, twigs and detritus. Cooked food can form mouldy gooey masses which houses different funghi and bacteria groups than those present in garden detritus.

There are a few reasons for not feeding cooked foods to worms (Eisenia spp.) in a smaller household size worm farm. It's not because the food is cooked but what it often contains.
The earthworm used in vermiculture is usually Eisenia fetida (red wigglers) though other Eisenia species are sometimes used. All Eisenia are epigeic species meaning they live in the junction of decomposing organic matter (such as leaf litter, aging manure, rotted fallen trees) and their natural food is decaying plant matter and bacteria that are also digesting the organic matter. They don't make use of small dead animals (meat and fat).
In large scale commercial vermiculture operations, leftover and past-due-date foods from restaurants, institutions, nursing homes and schools are used along with plant matter and carboard and paper. I'm not sure how they balance cooked foods but possibly much less is used than plant matter.
The fact food is cooked isn't the problem but what's in it and/or what happens to it when added to the bin. If you have leftover vegetables and fruit that's been cooked with no added salt, it's perfectly acceptable. A certain amount of sweetened cooked fruit is also fine as the worms will eat that too. But ready-made foods usually have preservatives, salt, fats and spices added. Either worms won't eat it, leading to odour caused by mouldy rotten food, or it can make them unthrifty and even killing off your worms if it's fed them repeatedly.
Fats and meat along with cheeses and dairy products will also not be eaten so shouldn't be used. Sites about vermiculture say onions and garlic can 'burn' the worms skin which is the problem with citrus fruit. They can be used but in very small amounts and should be mixed well with their other food.
Vermicomposting for Business, Farms, Institutions & Municipalities
Wormy FACTS and Interesting Tidbits about Eisenia fedita


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What is the probability of fixation for a mutant under fluctuating selection?
Here is an answer which explains how one can model the frequency of an allele that is under fluctuating selection (the selection that varies through time).
Not, thinking about fluctuating selection, there exist several derivations of the probability of fixation of an allele present at frequency $p$ with selection coefficient $s$ in a finite population of size $N$. For example, Kimura (using diffusion equations) approximated the probability of fixation $P_{fix}$ to be
$$P_{fix}≈\frac{1-e^{-4Ns} }{1-e^{-4Nsp}}$$
How to model the probability of fixation (in a finite population) of an allele that undergoes fluctuating selection?
I welcome one to answer by using whatever type of fluctuating selection. It might be an alternate of $s_1$ (uneven generation) and $s_2$ (even generation) or $s(t)$ might be a sinusoidal function of the time $t$ (in generations). Or $s$ might be drawn randomly from some distribution.


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How to calculate the conservation score of specific amino-acids or motifs in a multiple sequence alignment?
The proteins I'm interested in create disulfide bonds using cysteine pairs. In different states of the proteins, those pairs are sometimes formed, other times they stay separated.
I would like to calculate a score for the conservation of specific amino acids in my multiple sequence alignment (MSA).
The thing is that some of these amino acids or structures are irreplaceable. For example disulfide bridges must be conserved, otherwise the correct structure will not be adopted.
So, in some way, the score is already very high. But is there a way to calculate the score between different disulfide bridges?
Also, is there a way to state that a MSA shows an amino acid or motif to be highly conserved (as opposed to "just" conserved)?
Is there a quantitative way to differentiate the one from the other?

Are you looking at just the amino acid sequence, or do you have nucleotide sequences as well to compare?

there are many ways and terms that have been proposed for very conserved chunks of protein or DNA, e.g. ancient conserved region or ultraconserved region. However I think that it is more useful to just state the degree of conservation (100% identity, 99% similarity, etc.). There aren't really meaningful "conserved" vs "highly conserved" categories, and conserved in hominids vs. conserved in mammals vs. conserved in metazoans all mean different things.

nonetheless, your intuition is correct that disulfides are relatively conserved.

In my experience, many students new to sequence alignment want someone else to  put the results into a formula and produce a number that encapsulates the conservation of a sequence or the significance of an alignment or whether it is better or worse than some other one. You are correct in that a number (score) is required, but before I can provide an answer to your question (which I am prepared to do) I need you to tell me what you hope to use it for, e.g. to comment in a report, to compare two situations. And the situation for a single amino acid is different from a motif of several.

I now what you mean @David. We're looking at cysteines, some of them building disulfide bonds others not. We would like to understand how conserve this process is during the evolution of metazoan, but also of (much) earlier organisms if at all. we can see that some cysteine-pairs bond at specific conditions, other not. Is this possible (like you say) to piut a number to it? thanks

@AssaYeroslaviz If we can easily identify the cysteines involved in disulfide bonds, we can readily postprocess alignments and say that such cysteines are 90% conserved across mammals, 80% across vertebrates, 70% across metazoans (or whatever numbers), and then provide comparisons to various other residues. Is your question how do we postprocess protein alignments to give such numbers? Or is your question is it possible to define different degrees of conservation? Or perhaps even can we even estimate conservation from a multiple sequence alignment?

like the question stated at the top of this post state, I would like to know if it is possible to assign a score to specific AA (or also domains) from a Multiple sequence alignment. If the answer to this question is yes, then of course the next question would be how? thanks

I am still not clear precisely what you want to do. Look at my answer and then, if it is not on target, comment indicating precisely why.

I am somewhat disappointed after the effort I put in to trying to answer your question you have not responded to it in any way. As I believe that we are both professional scientists I find that somewhat uncollegiate.

Hi David, sorry for not responding. As we had here school vacation last week I took some time off work, so also tried to avoid reading my mails. I have not seen any posts from you. Thanks for this elaborated answer. I will read your it and let you know if I have more questions to that topic. thanks again

Preamble
I am not quite sure what the poster is trying to do, in particular the question “is there a way to calculate the score between different disulfide bridges?”. Clearly, if different bridges are completely conserved between species in two different proteins or within the same protein, that’s it. (Sort of the converse of ‘slightly pregnant’.)
Nevertheless this answer discusses ‘scoring’ multiple sequence alignments (MSA) and describing the results, so it can be updated in response to any clarification the poster makes.
The Clustal MSA program already scores positions in an alignment
I do not know what MSA program the poster is using, but the output from Clustal X (at least standalone v. 2.1 for the Mac) already presents scores of a sort. This can be seen in a sample output, below:

The height of the individual bars in the bar graph below the alignment ranges from a maximum (where all five sequences in this set align) to what I assume is the zero baseline (where one of the sequences introduces a gap).
Closer examination, however, shows that the scoring system used is not a simple percentage identity: 0, 20, 40, 60, 80, 100%.

In the detail it can be seen that (4xK + 1xN) scores higher than (4xV + 1xK), and also gets a ‘:’ comment (see below). This is presumably because it is using the same PAM or BLOSUM amino acid comparison matrix used in the alignment to compute the height of the bars. (I leave the interested reader to plough through the literature to see if this is documented.)
What can one say?
The question seems to wish to transform the numerical score into a descriptive statement. The following assumes that one is taking one sequence as reference — here 1qjo.
• The simplest possibility would be a statement of the type:

“P at position 8 in the reference sequence is completely (100%)
conserved in the data set, whereas at position 49 the conservation is
only 80%, and at position 51 only 60%”.
This could be converted to descriptions using the percentage scale in a subjective and arbitrary manner which one would have to define, e.g. >75% but <100% = ‘highly conserved’, >50% but <75% = ‘moderately conserved’

• An alternative would be to use the descriptive categories — * : . — and convert them to descriptive terms ‘completely’, ‘highly’ and ‘moderately’. This result of this would be different from using percentages. What one would really be describing here is not the conservation of a particular amino acid, but the conservation of amino type at a particular position. So the statement would be something like (choosing a different example):

“As regards the eight positions in the reference sequence where E was
found in the data set, only position 40 was highly conserved and
position 58 moderately conserved.”

Context matters
My example statements above all refer to “the data set”, emphasizing that any numbers or descriptions cannot be absolute, and their significance depends on the extent of the data set and whether it is biased towards sequences of a particular origin. The most obvious cause of bias is species e.g. a data set with 20 mammalian species and two insects. Not only species range is important, but it can happen that a problem is complicated by different forms of a protein in the same species, and that these forms may be more similar between species. A way of approaching the latter problem is to consult SCOPe, and if necessary construct a data set containing a range of SCOPe subcategories.
Other approaches to the disulphide bond problem
I am not quite clear whether any of the members of the family of proteins of interest to the poster lack cysteine at the position of the disulphide-bond forming cysteines of the references. If they do I would be tempted to use alphaFold to obtain predicted structures of these exceptional members and see if the positions at which the cysteines in the reference sequence occur are predicted also to be in close proximity in the exception.

I really appreciate your answer and I think it is a good start toward what I'm looking for. The two possibilities you offered sounds good. I'm starting to understand that it is not really easy (if possible at all) to get a number stating the degree of "conservativity".
I know about the ClustalO/Mafft/T-coffee/etc. results and the way they show how is conserve a position. But if I understand it correctly, this states only how conserved the position is by itself, and not compared to others.

I am not sure, if this is possible or even make sense at all. I'm interested though in trying to put a number to a specific position in the MSA compared to other positions. Or as @David put it. Is this one slightly more pregnant than the other one?
After thinking and searching the problem, I also see, that a structural comparison might give better (or at least more conclusive) results, as to whether or not a postion is more conserved.

The disulphide bridges I mentioned are a bit of a problem, because those Cysteines ** have to be there** in roder for the bride to exists. No cysteines, no bridge! Therefore they are always very conserved.
This is why, even though the answer is a good one to decide how to regard the question, your two suggestions will not really be helpful here, as they Cysteine-pairs will have most of the times 100%. So by themselves they will always be highly conservative. But how is it comparing them to one another?

So, maybe the question would be to see what around the bridges, maybe what is inside the loop the bridges create. If i can show that there are other, more unique AA there (e.g. W or Y), which might be needed for some kind a binding event, this might make this bridge "stronger conserved" than a bridge, where this AA is not available anymore, as the binding activity can't take palce anymore.
I'll take a look into AlphaFold and see if I can make use of it.
thanks


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Is UMI necessary when analyzing samples from Formalin-Fixed Paraffin-Embedded tissues?
We have FFPE-tissues we would like to use for a sequencing run. we think we can get enough biological material, so the amount of RNA shouldn't be an issue, but we're not sure.
A unique molecular identifier (UMI) corrects for PCR bias resulting from multiple PCR cycles, but if I have enough material, I don't need to do too many cycles. On the other hand the library preparation protocol using UMI is more complicated and error-prone.
So, my general question is

Is it always recommended to use UMI in a sequencing run originating from FFPE-samples, regardless of the amount of the RNA that can be extracted?

Is there anything in the literature concerning this problem?

I think you need to think about what you aim to gain out of the run? Expected outcomes alter how you should process the sample input.