text:
Is there any evolutionary reason for why some organisms (wrasse) change their sex in adult stage?
In San Francisco, I saw this fish:

and quoting the aquarium's page:

Part of the wrasse family, the California sheephead is a protogynous hermaphrodite. Simply put, all sheepheads are born as females, but eventually transform into males. Due to hormonal changes triggered by environmental and social cues, this fish can go from a reproductively-functional female to a fully-functional male.

I have never heard of something like this for any organism. Is this behavior unique?
But the real biology question is why they do that and not simply retain one gender throughout their life? In other words, what's the evolutionary advantage of such a weird approach?

This is not the only organism that does that. See https://en.wikipedia.org/wiki/Sequential_hermaphroditism. The wikipedia page also mentions some reasons for why such a phenomenon happens.

What you see is what you get (aka @WYSIWYG), would you like to post an answer? :)

I get what you say (:P) but I'll be merely repeating what is written in wikipedia. You can actually wait for a better answer. There are people here who would know about this topic better than me.

@WYSIWYG I only know because I had worked on such an editor when I was in Switzerland! :) Anyway, nobody seems to be able to answer, thus I would tell you to think twice for whether you should be posting an answer or not! If a better answer arrives later, trust me, I will check it up! ;)

@WYSIWYG You're probably better for judging this than me (you're a mod), but I'd say your WP link with a brief summary would be sufficient for now, and if a better answer does come along, we'll respect it as well.

Related Bio-SE question: Why are not all species hermaphrodites?

This is an interesting question.  This strategy is common among wrasses, but the Labridae is a rather huge family.  I found this article here that I think may help answer your questions:  http://faculty.sites.uci.edu/johncavise/files/2011/03/299-SexDev-herms.pdf

Please don't simply link to sources, but provide a summary or direct quotation of the relevant part as well.

That's silly, why write a summary of exactly what the paper says.

Because links die or change; because you could be pointing to anything; because people shouldn't have to read a full paper to find one minor point from it; because the guidelines explicitly say to do it ("Links to external resources are encouraged, but please add context around the link so your fellow users will have some idea what it is and why it’s there. Always quote the most relevant part of an important link, in case the target site is unreachable or goes permanently offline.")

No.  They're guidelines, not requirements, so lay off. He can click the link or not, no one else has provided an answer since 2016. I won't argue with you further.


text:
How many citric cycles are (can) working at the same time in one mitochondria?
Does one mitochondria has a limit of how many acetyl-CoA it allowes within his inner membrane to produce NADHs? And if, lets say 100 acetyl-CoA are in a mitochondria are they simultaniously running through their citric acid cycle or has the mitochondria also a limit for the amount of running citric cycles at the same time?

Seems the amount can vary, because the mitochondria's volume could vary.

source: Stack Exchange

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/

sort: votes


text:
Where does the first oxaloacetate comes form in the citric acid cycle?
Oxaloacetate forms together with acetyl-CoA citric acid. Now oxaloacetate is used but also re-used again in this cycle. But where does the first oxaloacetate comes from? Is that from the mother or produced by DNA or....?

Applicable for all biological cyclic reactions; and a molecular  egg-or-chicken situation. As all cells respire continuously, even when it wasn't born (it was its precessor-cells) , so we can't find any 'starting-time' or 'starting-moment'. Rather we could think-out how the OAA for world's first TCA-cycle, came?. You've pointed out a right paradox.

However, from another-view, there is no first-last in such a cyclic-reaction. We consider citric acid is the first-molecule because we've learned it that-way. But in some-other interpretation of reaction-networks; some-other compound is the first and some-another compound is the last. It highly depends upon how we view it.

There's not just one molecule of acetyl-CoA that's going through the TCA cycle. Every intermediate compound is present at a certain concentration, so there will be many oxaloacetate molecules per cell.
When the cell divides, it's split in two and the contents are also divided. So a new cell will also have many oxaloacetate molecules in it. This way the daughter cell can just keep running.
For the "first" oxaloacetate molecule we have to go back billions of years, and this would be a very complex question to answer. My guess would be that the first oxaloacetate molecule was produced by a non-TCA pathway, and the TCA cycle evolved later.

Great answer. I can't think this question being answered in any better way.

So each daughter cell would have less oxaloacetate? Less cycle input power?

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/


text:
Can some human groups evolve into new species?

The Sentinelese people are an indigenous people of the Andaman Islands, in the Bay of Bengal, an essentially hunter-gatherer society subsisting through hunting, fishing. There is no evidence of either agricultural practices or methods of producing fire.

Does such uncontacted people have potential to undergo peripatric speciation?
This link says

.......to the fact that the Sentinelese have lived in isolation for 60,000 years: genetically, therefore, there is a direct line between them and their pre-Neolithic ancestors.

Factors:
Geographical and Reproductive Isolation

They live in a  highly isolated and heavily forested Island in the Andaman sea.Any contacts with any other nearby Island has never been reported.

Differences with Mordern Humans
Wikipedia says that:

Behavioral modernity — a suite of changes in Homo sapiens behavior and cognition including abstract thinking, deep planning, symbolic behavior (e.g. art, ornamentation, music), exploitation of large game, and blade technology — is evident from around 40,000–50,000 years ago, and may have emerged abruptly then or may have arisen through gradual steps.

While Sentinels have been isolated for more than 60,000 years.

The Late Upper Paleolithic Model,  refers to the idea that, though anatomically modern humans first appear around 150,000 years ago, they were not cognitively or behaviorally "modern" until around 50,000 years ago. These authors note that traits used as a metric for behavioral modernity do not appear as a package until around 40–50,000 years ago. Klein (1995) specifically describes evidence of fishing, bone shaped as a tool, hearths, significant artifact diversity, and elaborate graves are all absent before this point.

Hints of Mutation:
This tribe miraculously survived 2004 Tsunami despite having small population.
This link says

Close to 150,000 people have been confirmed dead (due to Tsunami)... Sentinalese who live in the archipelago escaped unscathed because they took to the forests and higher ground well in time.
Scientists believe that because of the extreme isolation of the Sentinalese, this tribe has become biomedically valuable...... could be targeted by bio-prospectors for valuable genetic traits that may have long ago vanished in other ethnic or racial groups.

Strange courtship ritual

......this moment, a strange thing happened — a woman paired off with a warrior and sat on the sand in a passionate embrace. This act was being repeated by other women, each claiming a warrior for herself, a sort of community mating, as it were. Thus did the militant group diminish. This continued for quite some time and when the tempo of this frenzied dance of desire abated, the couples retired into the shade of the jungle....

If the island environment is very different from the other regions and some kind of environmental pressure selects certain traits then they may eventually give rise to a new species. That's how all speciation happened. But we can expect that it is not going to happen very soon. Stone-age humans are not a different species.

Could happen. The longer the isolation the more likely it will happen. Will take tens of thousands, maybe hundreds of thousands of years.

@WYSIWYG Speciation doesn't require that there is any difference in the adaptive landscape/selection - if isolated long enough simple mutation accumulation could render them as two different species.

@itachiuchiha there is a lot of text to the question and it would greatly benefit from being far more concise

Thanks for the suggestion. :) I tried to reduce the size a bit.

@rg255 ..and specially mutation in genes coding for ZP proteins, which allow the ovum to bind sperm. Important mutations could aid in the development of prezygotic speciation, which is easier than postzygotic speciation (where fertilization does occur, but large chromosomal differences prevent further development).

Absolutely it is possible for the current human species to evolve in to two distinct species in the future. Barriers to reproduction, such as physical isolation, help the process along as it allows differences to accumulate. Gene flow allows hybridisation (not in a species to species sense, but sub-population to sub-population sense) which will impede the process of speciation because it allows genetic variation which is unique to one population to move to the other.
Differences occur between populations, which can lead to speciation, by the mechanisms of evolution - mutation, migration, drift, and selection. Different mutations occurring in sub-populations allows the two to become genetically incompatible, leading to speciation. Gene flow from a third population may make the first two too different to reproduce (see also ring species). Drift and selection may cause genetic variation which allows reproductive compatibility between two populations to be lost, further generating genetic differences. Selection in different directions (e.g. the environment of the two populations is very different) can hasten speciation, as seen in a classic Drosophila experiment.
Will the population you mention ever become a non-human/novel species? Who knows, but they are certainly interesting - as you've realised, their isolation by geographic barriers will help differences to accumulate between them and other human populations that could lead to speciation.
I suggest reading more about evolution and speciation here!


text:
How does action potential conduct across a branch in a neuron?
As the action potential travel in the dendrite towards the cell body, it will encounter many branches. What happens at the branch? What makes it go to the cell body instead of other dendrite?
Also, as the action potential travel from the axon to its branches, does it go to only one or all terminals? If it goes to only one terminal, how is it decided which terminal it has to go?

Awesome question!  Thanks for asking it and giving me the motivation to look back at the literature to increase my own understanding!
I do want to point out one issue of semantics before starting.  Just to avoid confusion, I'm going to follow the example of some of the well-known experts in this field and distinguish dendritic spikes from action potentials.  The main difference is that a voltage spike in a dendrite or dendritic spine will experience attenuation (essentially a weakening of the spike) as it propagates toward the cell body, and it is distinct from the all-or-none voltage response of an action potential.  It is generally accepted that action potentials are initiated in the axon (hillock) because that is where dendritic and somatic spikes will ultimately sum to fire the all-or-none voltage response.  I just want to clarify what I mean by dendritic spike when I use it during this explanation.
What happens at the branch? So, to answer your first question, you're absolutely correct that when a dendritic spike occurs, that spike will encounter multiple branch points along the dendrite as it proceeds toward the soma.  When a spike propagates to a branch point, the properties of the branches determine what happen to the spike.  One important property is referred to as the geometric ratio (GR).  This property was described Goldstein and Rall in 1974 (manuscript here for review https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1334570/) and the gist of the equation is that spike attenuation is dependent upon the diameter of the branch the spike is coming from and the branch the spike is going into.  The concept behind this is called impedance mismatch, but that's complex and I won't get into it.  Just know that spike propagation is favorable from a large to a small branch, but is not favorable from a small branch to a large branch.  If you wish to read more about this concept, I'd recommend the Goldstein and Rall paper referenced earlier and chapter 14 of the textbook "Dendrites" by Spruston, Stuart, and Hausser.
Additionally, the presence of leak or voltage-gated channels in that branch can determine how well the spike will propagate or how much attenuation will occur.  This is an easier concept to grasp because the idea is essentially that more channels open when the spike passes through that branch, the more charge leaks across the membrane and causes attenuation of the spike.
All questions regarding preference of flow To sort of attempt to answer all your other questions at once, nothing really forces the spike toward the soma or a specific axon terminal.  There are dynamic changes in membrane potential that may prevent spike propagation down one branch or action potential propagation in a certain direction (like how action potentials aren't thought of as propagating from the axon to the soma because of the hyperpolarization and long inactivation of sodium channels at the area that just fired, preventing what is called backpropagation at that particular time).
I think a little reading on neuronal cable theory might be of some help with this question too.  This link is to a PDF that gives a pretty brief explanation of this concept https://nanohub.org/resources/20112/download/Lecture1_Passive_Conduction.pdf.  This is a pretty math-heavy field, so beware if math isn't your favorite subject!


text:
Why does the nerve action potential needs potassium?
When looking at the action potential generation I do not understand why potassium is needed. I know that potassium is used to repolarize the cell. But why are sodium channels and/or sodium pumps not used to push the cell back into its resting potential?
For example in this video at minute 2:00, sodium is pumped in, and potassium out of the cell. But both are positive ions. You get a less negative membrane potential but wouldn't it go faster if the potassium ions stayed in the cell?
Has potassium an extra property compared to sodium that makes it especially suitable for the repolarization step?

The action potential is mediated by the opening of Na+ channels, which happens in the order of milliseconds (e.g., Aldrich & Stevens (1987)). Repolarization occurs through the opening of K+channels. Their opening is delayed by a few milliseconds (Purves et al., 2001) to allow Na+ to pour into the cell through Na+ channels. After that delay, the opening of K+ channels occurs also in the order of milliseconds. After these two processes are over, the membrane enters a refractory period, again on a millisecond scale. Then the membrane is ready for another action potential.
The Na+,K+-ATPase, on the other hand, has nothing to do in the action potential process as such. It operates much more sluggishly and it can by no means keep up with the rapid channel gating during action potentials. Instead, the Na+,K+-ATPase activity operates at the background to maintain the overall ion homeostasis. As an analogy, the power adapter of a laptop PC can never keep up with the processor speeds; instead, it functions in the background keeping the battery charged.
Then why two different ions? Because two different species of ions are necessary because they fulfill opposite roles in terms of polarization and reploarization.
References
- Aldrich & Stevens, J Neurosci (1987); 7(2): 418-31
- Purves et al., Reconstruction of the Action Potential. In: Neuroscience, 2nd ed. Sunderland (MA): Sinauer Associates (2001)


text:
What kind of snake is this?
First, we are located in Missouri. In between St. Louis and Cape Girardeau. St. Francois county to be precise.
We just walked outside and found this on the porch so we carried it off. Normally this wouldn't be a big deal, but we have a little one now and I didn't want to take any chances.
The snake, pictured below, was approximately 6 inches long. He seemed timid in nature, he didn't let us get very close to him before he started to slither away.
I assumed he was a juvenile black rat snake, from my highly deductive google searching, but I also know that snakes sometimes change color, shape and design as they get bigger. So I wanted to find out if my guess was correctly or completely mistaken. Thanks for you help!

Great find!
I'm pretty certain that is actually a Prairie Kingsnake (Lampropeltis calligaster - likely the subspecies L. c. calligaster).  The biggest indicator to me are the two alternating rows of dark spots on sides, with some blotches fusing.  They are distributed all over Missouri, although pretty rarely seen due to their microhabitat:

They tend to be fossorial, spending much of their time underground and
out of sight. As a result, there is little known about the biology and
status of these secretive snakes. Most [prairie] kingsnakes are observed
hiding under boards or other debris or crossing roads on warm
evenings.

I actually used to study herpetology in St. Louis, and we caught a few of these.  The juveniles tend to have well defined spots that fade in time, although there is some degree of polymorphism here.  Looks like yours is somewhere in between.  See pictures below for reference.
Juvenile:

Adult:

Worth mentioning these snakes are nonvenomous, and typically docile.
Photo cred: Edward Prenzler


text:
What are these two insects (or at least one of them)?
I need to catch and identify insects for my biology project, but I cant identify those two bugs.
Can I get the genus and the species (or it can be just general name of what this type of bug is called?)
They were found in Chicago suburban area.

Can you add a short description for their morphology is not very clear to me,especially the second one? Has it got wings?

This question should be splitted, because now you cannot except both right answers.

I the first insect is a cricket, female Fall Field Cricket,Gryllus pennsylvanicus.

It is widespread across much of North America.They are  often found around areas of human habitation.
The the coloration ranges from dark black to dark brown, although some specimens show a slight reddish tint. The black antennae tend to be longer than the body span of the species.

It is a female because it has a long blackish brown ovipositor.

References:

Wikipedia

pbase.com

bugguide

Thanks! I also found the second insect and answered in another answer. I gave you best still..

After tiring hours of research of not knowing what even is the second bug's order I've finally found the second bug as other part of the answer.
The second bug is Slender meadow katydid, Conocephalus fasciatus from order Orthoptera, also a female.

The green abdominal projection is its ovipositor.


text:
How to calculate the number of folds present in a protein
Suppose I have number of PDB files of proteins. How can I get the number of folds present in these proteins? Is the fold count derivable from the PDB files? If so, how?

How do you calculate a fold? Amino acid residues in a protein in vivo always have some angle between them - the carbon backbone is never in a straight line. I'm afraid this question is far too broad.

Do you mean 'fold' as in the topology? So alpha-beta-barrel, sandwich, key-barrel, etc?

@gilleain yes exactly...

There are various ways that you could do this.

CATH is a hierarchical classification system
SCOP is another such system with a different hierarchy
PTGL is the protein topology graph library
Tops motif will scan PDB files and match patterns against it

How you actually apply these tools or lookup within these systems is documented on their websites. However, it depends on what you want to do - look up published structures, or new experimental data.
I should point out that writing software from scratch to determine the fold of a protein may be tricky.

this is what i wanted to know... writing from scratch would be difficult....


text:
Are ITS1 and ITS2 good for divergence time estimation?
I had a discussion with a colleague who told me internal transcribed spacers (ITSs) are not good for divergence time estimation:

Because they are non protein coding genes;
Because they belong to a gene family.

However, I was not able to find anything in the literature about that. Can someone please enlighten me?


text:
Is Hemoglobin binding to oxygen the same as Adsorption
I have recently been reading about Hemoglobin and came across how it binds to oxygen. This seems very similar to Adsorption. Is the process of Hemoglobin binding to oxygen through Adsorption ?

I’m not about expert on this topic but from what I know the binding of oxygen to heme groups is a phenomenon of complexation, not adsorption.

From the Wikipedia article you cite the answer to your question is clearly NO. They seem very different: absorption is described as a surface phenomenon, whereas oxygen binding occurs in a single internal pocket in each globin subunit and forms a specific bond to an Fe(II) atom. The chemical nature of this pocket is quite different from that of the surface of the protein.
The Wikipedia article states:

Adsorption is the adhesion of atoms, ions, or molecules from a gas, liquid, or dissolved solid to a surface.[1] This process creates a film of the adsorbate on the surface of the adsorbent.

and

Similar to surface tension, adsorption is a consequence of surface energy. In a bulk material, all the bonding requirements (be they ionic, covalent, or metallic) of the constituent atoms of the material are filled by other atoms in the material. However, atoms on the surface of the adsorbent are not wholly surrounded by other adsorbent atoms and therefore can attract adsorbates.

However if you consult a text-book which describes the biochemistry of haemoglobin, such as Berg et al. you will find the specific chemical nature of the binding clearly described, as indicated by this extract:

The iron atom lies in the center of the protoporphyrin, bonded to the four pyrrole nitrogen atoms. Under normal conditions, the iron is in the ferrous (Fe2+) oxidation state. The iron ion can form two additional bonds, one on each side of the heme plane. These binding sites are called the fifth and sixth coordination sites. In hemoglobin, the fifth coordination site is occupied by the imidazole ring of a histidine residue from the protein. In deoxyhemoglobin, the sixth coordination site remains unoccupied...The binding of the oxygen molecule at the sixth coordination site of the iron ion substantially rearranges the electrons within the iron so that the ion becomes effectively smaller, allowing it to move into the plane of the porphyrin (Figure 10.19).

The only similarity I can see is that in both processes the interaction of the gas with the material to which it binds is controlled by the pressure of the gas. However in the case of haemoglobin there is a distinct difference from absorption in that the dependency on pressure exhibits a sigmoidal curve, specifically suiting it for the role of quantitative delivery of oxygen to the tissues at a particular small reduced pressure range.
You sound as if you come from the physical sciences. If so, prepare to be surprised at how smart a chemist Mother Nature is.


text:
Same primers and different melting peaks for two samples (~1°C appart)
In the figure, you can see that melting peaks differ by ~1°C at each sample.
Should I be worried?

I would have said that 1⁰C is not a significant difference but the technical replicates are so perfectly matching!! Are these samples from same source (tissue/cells etc)?

they are the same tissue (oviduct) from two different animals

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


text:
Is the BMJ a reliable source for biology studies?
The BMJ published the Wakefield study, criticised it, and retracted it. They then argued that the Wakefield results they published were fradulent. Is BMJ reliable for biology studies or is it an anti vaccine conspiracy journal?

The Lancet published the study, the BMJ are the ones that exposed its fraudulence.

First: The infamous study by Wakefield et al., was published 1998 in Lancet, see here. Wakefield had indeed falsified his study, by selecting kids with certain preconditions, taking money from attorneys (and not disclosing it) and others. Here is a nice overview over it.
To your question: The British Journal of Medicine (BMJ) is indeed a reliable and credible source for scientific articles, as is the Lancet. Journals can check the content they get for publication to some extent, but if they have authors who deliberately falsify studies, then they can do little. The thing which can be criticized in the Wakefield case is the time that it took to withdraw this publication.

But there would be obvious inconsistencies if the results were fake.

If these are obvious, journals will most likely not accept the article. See pubpeer...

BUT they accepted wakefield

@Bobb so what's your point? I could write a paper with completely falsified data, add some collaborators who generated their own and described it truthfully enough, write a convincing but incorrect conclusion, and get it published in a mid to top tier journal. If someone is smart enough, they can get around the current checks in the system unless an incredibly thorough review is done and the results are essentially independently generated again, which almost never happens before publication. There is, and always will be some level of trust in the system, otherwise nothing would get published.

Hmm. Sounds like peer review is almost useless.

@Bobb Exactly as MattDMo says. There are pther cases, like the one of Olivier Voinnet who recently had to retract 7(!) papers and correct at least 15 (I lost track here) and return prestigious prices. This guy was once a star, but has now fallen. See ]here.

Peer review has it's drawbacks, and they are known. The problem is, there is no better system available. And still: Almost all papers are ok.

@Bobb tell me, are you a scientist? Do you actually understand what the peer review process is? Have you ever submitted a paper for publication to a halfway decent journal? If not, you very likely don't know what you're talking about. No one who actually knows what the process is and/or has been through it would say it's "almost useless." And if it is useless, what's your better alternative? I'm sure you've thought that through very carefully...

@Bobb if you're just here to troll, you will very quickly find yourself banned from the site, and potentially all Stack Exchange sites. If you want to engage in a thoughtful conversation about the pros and cons of the current system and how it can be fixed, fine. If you're just going to make asinine comments displaying your obvious ignorance about the subject, you may as well just leave now.

@Bobb peer review is good at identifying scientific quality but less so at detecting deliberate fraud. This is fairly well understood within the community (https://www.elsevier.com/reviewers-update/story/peer-review/as-peer-review-week-2016-begins,-our-infographic-highlights-what-researchers-really-think-about-the-current-process/) and is one motivation for the Reproducibility Initiative (see also http://academia.stackexchange.com/questions/74761/who-is-supposed-to-repeat-experiments).

+1 for the important point, that the problem was how long the study took to be pulled and the fact that the Lancets own investigation was so poor another journal had to show its fraudulence.

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


text:
Why is Lamarck's evolutionary theory considered incorrect?
Many sources postulate without much argumentation that Lamarck's evolutionary theory is "obviously incorrect". A classic example provided in such sources is the one with giraffes, in which Lamarck argued that the necks of these animals became long as a result of continually stretching to reach high foliage. This mechanism for adaptive change in response to the environment is considered wrong.
Now the counterargument to Lamarck's ideas comprises modern findings in genetics. So it is stated that organisms pass down traits through predetermined genetic information, not based on environmental adaptations during their lifetime. Furthermore, genetic research shows that living organisms cannot alter their genetic material as needed.

Doesn't the latter contradict the evolutionary theory itself, which states that nature (i.e. environment) shapes species through natural selection in the environmental milieu? If it is not the environmental/natural factor that is responsible for genetic evolution, then what is?
If genetic material were to be unchangeable, then how would adaptation to the environment and consequent evolutionary change would ever be possible? The genotype (following this logic) would remain the same.
And lastly, maybe giraffes do not develop long necks at such a rapid pace (as Lamarck probably thought) by simply stretching their necks in one generation; however, what, if not neck stretching, is responsible for their consistently longer necks throughout thousands or millions of years? Hadn't the environment gradually shaped their genotype? Similarly, if I run more often, maybe my children will not become more fit, but isn't it just a matter of time (thousands of years) that if all of us consistently run a lot, then our offspring will eventually become more fit? Wouldn't our voluntary efforts eventually enhance our genetics? I do not see any problem with Lamarck's logic at all, except probably the time frame.

PS I became inspired to ask this after reading this, this, and this, plus after consolidating a few of my own memories from bio classes

Welcome to Biology.SE. Your question could be summarized into "How does evolution work?", which is a broad question which answer can be found at many different sources online. I would recommend that you have a look at Understanding Evolution (UC Berkeley) which is a short and very introductory course to evolutionary biology.

You can have a look at plenty of very introductory posts on Biology.SE as well such as the answers to this post for example.

In science theories are tested by experiment evidence and, as scientific knowledge progresses, how they can be accommodated in the framework of knowledge. In brief, there is no evidence to support Lamarck’s idea (Lysenko is notorious for his falsification of such evidence during the Soviet era to fit with Stalin’s philosophy), and the subsequent discovery of the molecular basis of heredity provided a requirement for the theory to show how changes in somatic cells could affect the DNA of the germ cells. No such evidence has emerged.
It is true that there are epigenetic effects, but none so far support Lamarckian postulates of the giraffe neck variety.
Finally, a word of advice. Don’t waste your breath on this list with arguments of the sort “Doesn't the latter contradict the evolutionary theory itself”. This is not a philosophical debating society, but community that is concerned with the factual basis of science. If you have never studied molecular sciences, stay away — or ask questions in the course of genuine attempts to acquire knowledge in this area.

I think you misunderstand both Lamarckism and other descriptions of evolution such as the modern synthesis (Darwinism with Mendelian genetics and a few bells and whistles). Both theories accept organisms have heredity with occasional changes. Neither Darwin nor Lamarck knew about genes, so I'll explain what their ideas boil down to in modern language.
In the modern synthesis, frequent changes called mutations may increase fitness (we call these beneficial), preserve fitness (we call these neutral) or decrease fitness (we call these deleterious). Mutations happen because DNA isn't perfectly copied or maintained; there's no bias in favour of beneficial mutations. However, as generations pass beneficial mutations proliferate, deleterious ones disappear (unless continually generated by mutation asymmetries, and even then they'll be rare in the population), and neutral ones' frequency in the population "drift" at random.
In Lamarckism, mutations are preserved based on beneficial acquired characteristics, which would require a way for bodies to identify which acquired traits are useful (injuries aren't!), reverse-engineer the genetic changes that would achieve them (which is basically impossible because DNA is more of a recipe than a blueprint), then update gametes with these changes. There is a lot of evidence that supports Darwinian evolution ("natural selection") but not Lamarckian evolution. For starters, Lamarckism couldn't explain novel biochemistry.
Biologists such as Richard Dawkins (see e.g. Darwin Triumphant, a chapter of A Devil's Chaplain) have pointed out that, even if there were life that could do what Lamarckism requires, it would not only still be susceptible to natural selection, but could only perfect a viable Lamarckism mechanism of discriminating good changes from bad by the action of natural selection. In other words, even if Lamarckism happened it would be an emergent property of Darwinism, not an alternative to it.

Nice answer, but you should also add some references in your answer for further reading by anyone interested.

@another'Homosapien' Partially addressed in my edit.

"there's no bias in favour of beneficial mutations." I wonder though, is this based purely on the theory, or is this an inference from empirical data. Because theoretically it is not impossible for positive mutations to get favored (via genetic interactions).

@rus9384 You can think of it as an assume-fewest-empirically-required-entities version of theory. If someone discovers a gene tomorrow that biases mutations in its organism to be favourable, that'll become an oh-all-right-then footnote.


text:
How far is stem cell research from being to generate a new organ?
How far are we from being able to use stem cell research to generate a sperm, a heart, a liver, and a kidney?
In stem cell research, my understanding is that you must start off with some cell to initiate the process. Can this be any cell, or must it be an embryonic cell made out of a sperm and an egg?

What is the measure of "far"? How can anyone tell when in future will something happen? It may happen tomorrow or not even in 10 years.

Sperm can already be generated using stem cells http://blogs.discovermagazine.com/d-brief/2016/02/25/scientists-grow-working-sperm-from-stem-cells/#.V-UADBV94o8
Also, heart, liver and kidney cells as well.
http://www.popsci.com/scientists-grow-transplantable-hearts-with-stem-cells
http://www.ncbi.nlm.nih.gov/pubmed/26458176
Full organs are still far. The main problems are to grow them separately from the rest of the body (embryonic development) and to vascularize them.
One solution is to grow them in other animals http://www.dailymail.co.uk/sciencetech/article-3442818/Growing-human-organs-farm-creatures-takes-step-closer-New-guidelines-allow-research-human-animal-hybrids.html
There are experiments done with some success in using "decellularized" kidneys as a scaffold to "grow" a new kidney by perfusing stem cells into it. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4927010/
There are the so-called organoids, very little agglomerates of different organ-specific cells differentiated from stem cells. They are far from being functional organs but it's definitely a start. http://hub4organoids.eu/organoid-technology/
Some labs are experimenting with 3D printing. They use stem cells to derive all the organ-specific cells needed and then they try to rebuild a functional organ by printing cell by cell, layer after layer. http://www.nature.com/nbt/journal/v32/n8/full/nbt.2958.html
Lastly, embryonic stem cells are not strictly needed anymore, they can be substituted (in most of the cases) by iPS that can be derived from many different adult cells (i.e. no embryo is needed).


text:
Do housekeeping genes vary between tissues
I am working on an RNA-Seq project, and I am aware that some researchers use housekeeping genes as a method of normalization.  My project has several different tissues, and I was wondering if housekeeping gene expression is generally invariant across tissue type?

There is no such thing as a universal housekeeping gene.

My experience is: Yes they can vary quite a lot (according to differences in the genetic profile of the cells) and you have to test this. As a primer I can recommend reading the articles listed below. These are mostly looking into this in the context of realtime PCR, but this should be valid for RNAseq as well. For some applications it is also a good idea to use more than one gene for normalization.
References:

Accurate normalization of real-time quantitative RT-PCR data by
geometric averaging of multiple internal control genes.
Selection of housekeeping genes for gene expression studies in human
reticulocytes using real-time PCR
Reference Genes / Housekeeping Genes
Gene Ontology Based Housekeeping Gene Selection for RNA-seq
Normalization

It depends on the definition of housekeeping genes.
ENCODE recently released RNA-seq of 17 tissues at 8 developmental stages.
A list of housekeeping genes was also provided.
They are not exactly constant. They just are less variable than other genes.

Your answer sounds as if it may be correct, however in order for the reader to find out he needs to go to an external site. It would be more useful, and more in keeping with our model if you could flesh out your statement "They are not exactly constant" with some representative examples, which would enable us to upvote your answer. The interested reader (the poster has presumably finished his project now) can follow your link for full details.


text:
RNA-Seq library normalization and experimental setup
I'm working on an RNA-Seq project and I am trying to figure out library normalization.  I'm aware of using the geometric means (e.g. cuffdiff) of the fpkm for the normalization.
However, I was wondering why people don't add some unique, known RNA sequence of known concentration into their sample prior to amplification.  Then after sequencing you would have some known measure by which to normalize your fpkm. I would think this would also be a way to minimize batch effects.
Is there a technical reason why this isn't done?

People do do that. Google "ERCC spike-in probes"


text:
Can organisms like Noctiluca be commercially exploited?
Scientists think that Noctiluca flashes to startle or scare away its predators. The bioluminescence might also attract bigger predators to eat Noctiluca’s predators, just like a burglar alarm that alerts the police to come to someone’s house to catch a robber.
 It takes energy to make the chemicals that allow them to glow. It would be a waste of that energy to glow during the daytime
But the question is whether we can commercially exploit this for human welfare??

Well, scientists have been developing Bioluminescent Plants to use as a future road light source. Also, there is a way that Bioluminecent algae can be used as medicine.


text:
What makes a 'sense'? Is fatigue (tiredness) a sense?
I have watched to new episode of Scishow on that scientists added 3 new senses (Thermoception, Proprioception and Equilibrioception) to our 5 sense list, and was wondering what makes a 'sense'?
Wiki definition:

A sense is a physiological capacity of organisms that provides data
  for perception.

Does that mean fatigue (feeling tired) is a sense too?

Well, some guys consider we have as many as 21 senses. I don't think tiredness can be considered a sense, it can be partial inhibition of all senses. You might want to read my answer to know more about tiredness.

I would think "fatigue" is a state, which the other sense alert you to due changes away from homeostasis

@another'Homosapien' beside that-21 with known-receptors ;  I think as the "feel"s of "joy", "sorrow", "fear" etc as specific, clear-cut fundamental  senses (not mere some mixture of other senses), and on same way, "time", "space", "number", "shapes" etc. Also Wikipedia have articles on "time perception" (https://en.wikipedia.org/wiki/Time#Time_perception and https://en.wikipedia.org/wiki/Time_perception).

I feel many sort of fatigue. For say after running or such physical task I feel a mixture of "Pain+Heat+partial inhibition of mental activity (But not sleepy)". After cramming a long dull text I feel very sleepy. After performing a big arithmetic calculation I feel some inhibition of mental activity (but not sleepy) + some pain in eye, neck and various part in head. After end-part of a long tour-program I feel a mixture of Lack-of-appetite+anxiety+sleepiness. After a sleepless night beside a hospital, I feel vomit + increased level of alertness + No sleep.

To me, the defining characteristic of a sense is that it assimilates information from the external environment for your body to use if necessary. This is also the way the textbooks I've taught from treat it.  Thermoception senses external temperature, your body evaluates and, if need be, you take action. Equilibroception senses gravity to help you evaluate your orientation with respect to the Earth.
Proprioception is a hard one to categorize. Some of what is classified as such seem to rely on only internal sensors such as how much a muscle is stretched. Other aspects of proprioception rely on muscle tension which would indeed be affected by gravity and qualify proprioception as a sense by this definition.
I would say fatigue is not a sense because it is based on internal messages. How about a "sense of hunger"? I'd again say no, hunger is also the result of internal messages. Your sense of smell can lead to hunger but the information gathered was odor, not hunger.


text:
Portal Systems in Humans
I was reading about nephrons in my physiology book when i came across this-
The efferent arterioles and peritubular capillaries technically constitute a portal system
But according to Wikipedia, renal portal system is absent in mammals. Can someone please explain this contradiction?
Edit 1: Could it be that humans are an exception to the case and do contain a renal portal system?
Edit 2: When we were discussing this in class, the my lecturer did say, "They are like portal sytems."
Why is human renal portal system not considered a portal system? Although, it connects two capillary beds (efferent arterioles and peritubular capillaries)
Edit 3- Some sites do say that the capillary beds that connect generally belong to different organs. Could this be responsible for exclusion of human renal portal sytem?

I think it is a semantic disagreement. Your physiology book says "technically", which suggests that the author knows the renal capillaries are not the same kind of "portal" system found elsewhere. Humans are not exceptional mammals.

@kmm point taken, but what differentiates it from a portal system?

You should ask your lecturer why they say "are like a portal system" and not "are a portal system". The distinction seems to matter to them. I don't care much for semantic details.

Unfortunately, my lectures on the topic have already ended and currently it is our prep time for the examinations. I know this to be just another semantic disagreement but I am curious to find out why.


text:
Is bad tasting food more likely to cause harm?
Taste is often referred to as subjective. For example certain foods taste bad to me, such as oranges, grapefruit, grapes, raisins, and sweet potatoes. However the wiki article on taste explains that from an evolutionary perspective, it's important that bad taste might indicate poison in the food; taste isn't an arbitrary matter of subjectivity.
With that in mind I pose the question if a food tastes bad to a particular person, is it more likely to be causing harm to that person than someone who finds the food pleasant? In other words, is the bad taste a sign that my body is not suited for some components in the food?

I vaguely remember a documentary saying that the bitter taste experience may have evolved as an anti-poison mechanism, for example when tasting new berries. Often poisonous ones are bitter. But cyanide tasting of pleasant almonds, or people disliking broccoli are both different - taste is not linked to harm/benefit. We did not evolve with cyanide, and broccoli doesn't trigger the strong "bitter" taste but is rather a childish preference.

@James you could write an answer. My answer was in same logic as your comment; however had poorer examples and no reference.

@AlwaysConfused My answer wouldn't add much more than the comment. Some fowl tasting food is great for our health, some very tasty food will harm us when over-eaten for years, and some tasty or tasteless compounds are actively harmful, and in all the previously mentioned statements there are exceptions! Too broad for my liking.

Why on earth has this question picked up two close votes for a medical question?!

Take a look at this article: https://www.ncbi.nlm.nih.gov/pubmed/25286017 I hope you can acces it. @AlwaysConfused this article is consitent with your answer, citing this would imporve your answer.

LaLanne said his two simple rules of nutrition are: "if man made it, don't eat it", and "if it tastes good, spit it out.".

@RickBeeloo Thanks for the reference you provided. I'll go through it thoroughly anD will use it as a citation thank you

@RickBeeloo aww its not free access and  so i cant access it right now. Thanks for your help.

tl;dr; If someone likes a food item, then even if it taste not so great to you, it will probably not harm you. If a food item taste awful to everybody (in particular bitter), then it would probably be best to avoid it.
Taste perception per se is not subjective, you either can detect or not a defined compound at a defined concentration. Food preference however is of course much more subjective.
The most established theory in the field is that we evolved both bitterness and sourness as a warning signal for poisonous compounds and inedible food. Bitterness is often the most referenced as most poisonous substances taste bitter to humans (e.g. strychnine, nicotine, ...) and are detected at very low concentrations (in the nM to $\mu$M range) (Meyerhof W, 2005). In comparison, the threshold for sweet taste perception is well above > 100mM (Park DC, 2015), or put otherwise, humans are at least 1000x more sensitive to bitterness compared to sweetness. As a result, we evolved to detect small quantities of bitter compounds and to dislike food items that are bitter as they could be poisonous.
Now for your question, you are probably misusing the word taste when you meant flavor, which is a combination of both taste and aroma (i.e. taste perception and olfaction combined, for example the "taste" of a banana). Food preference varies from people to people based on both genetic, physiological and more importantly environmental factors, in particular food habits. Typical examples are spiciness and saltiness where you can slowly adapt to tolerate higher and higher concentrations, meaning that your own food preferences can shift over your lifetime. Another illustration is the common shift in food preferences between childhood and adulthood. In other words, food preference is not an excellent predictor of a harmful food item.


text:
Can/Do any spiders "release" their own web in the presence of a threat?
Preface
We live in the north eastern US and have a spider that has setup shop next to our front door.  I've lived in this area my whole life and she's the largest spider I've seen.
We're too interested and afraid to do anything but let her be, so we've been watching her for the last couple of months.
The "Event"
My wife almost bumped into her web while we were looking for our cat tonight. (I mean she was really close). The spider was hanging around in the center of the web at the time.  A short while later my wife saw the spider scurrying furiously and then she crawled back into her hiding spot behind the shutter.  Next time I looked over, her web was completely gone - neither of us think we got close to it again during that short time.
I'd also like to point out that it was a bit gusty tonight, a rain storm was probably about an hour away.
We are wondering if something happened to her web, or if she took it down intentionally.  If she did, is this behavior common in spiders?
Other Information

She's got a blackish/yellowish bulbous body with the same color striped legs
She's about the size of a ping pong ball (including legs)
She hides during the day behind the shutter, but always comes out when the sun starts setting.
Unfortunately I have no pictures of her that aren't the underside, she never comes around the front of her web.
She builds a "classic" looking web, a hair longer than a foot in diameter with a couple of longer guy lines out to the door and the stoop. There are never any messages written in it.
She either never catches anything, takes her food back into her little den, or eats very quickly because I've never seen anything wrapped up in her web.
Our cat found his way home a couple of hours later

Photo

Thanks!

Do you wish to get your spider identified? I ask it because it is nowhere mentioned in your question and it has a tag species-identification.If you intend us to do so maybe you should add that part too. Welcome to BioSE. :)

OP used a term 'she' to describe that spider. ("She's about the size of a ping pong ball (including legs)"). Was it a female spider?

"Can/Do any spiders release their own web in the presence of a threat?" or "Can/Do any spiders destroy their own web in the presence of a threat?" ... which one you are asking? since you've wrote "she crawled back into her hiding spot behind the shutter. Next time I looked over, her web was completely gone... We are wondering if something happened to her web, or if she took it down intentionally. If she did, is this behavior common in spiders?"

I've also seen several times (but then I was a kid), if I disturb a spider who is weaving a web; it ruptures own incomplete web before leaving the place. (But I can't conclude it is their behavior or just coincidence, also their species was not-identified, normally)

@SanjuktaGhosh Thanks for the welcome! And sorry for the ambiguity - I was mostly interested in the web tear down, but I was not sure if it was specific to the spider species or not so I included as much info as I could.  I am not aware of the species so I figured if anyone identified it it would be a bonus :)

Building a web costs a lot of energy. From Wikipedia: "It is common for spiders to eat their own web daily to recoup some of the energy used in spinning. The silk proteins are thus recycled." https://en.m.wikipedia.org/wiki/Spider_web

Interesting! I had no idea

This is an older question, but just for the information, here are a couple of points that might be helpful:

Some (not all) spiders do tear their webs down and 'recycle' the silk when the web has been damaged to the point of being unsuitable as a snare.  I don't know if any spiders simply cut the web loose and let it fall if they're disturbed, but I would doubt it - perhaps the gusty wind did something?
You were right - it is a 'she'; a female Araneid of some sort, to be more precise - the candy-striped legs and orbweb tell you what she is, and the large abdomen and general size tell you she's a female.  From the photo I can't hazard a guess* as to which spider, or group of spiders, within that general category she might be, but she is an orbweaver of some kind.  You didn't ask, but since all known orbweavers are completely harmless to people, she is too.
Some of the larger orbweavers in this group can get quite large and spin very large webs.  The largest I ever had made an orb about 3' across on a structure which stretched from the eaves to the ground, or about 10' top to bottom.  Her abdomen was maybe a bit large than an inch across, and with legs included, she would have been rather larger than a pingpong ball.  I used to feed her various things I found, and I discovered that she would happily eat small toads as well as large insects.

I include a link to one of the orbweavers which have that red tarsus - unfortunately, there are more than just one orbweaver with that feature, but if I was pressed to offer an ID, I'd go with this one provisionally:  Neoscona crucifera.  These Barn Spiders (and there are at least two spiders known by that name..) can get quite large, and make a reasonable fit with your photo.  The reddish color on the tarsi is fairly dull, not a bright red, so I lean away from N. domiciliorum and other orbweavers that might turn up in your area, although of course I'm not a fanatic about it..
https://bugguide.net/node/view/28154
*well, I guess I wasn't completely honest here..


text:
These Mammals Had a Good Run, So What Happened?
One of the great mysteries of the mammals is that some of the longest-lasting just aren't with us today.  The list of these puzzling unfortunates is as follows:
Paleomerycidae

DURATION:
55.8 to 4.9 million years ago
Hyaenodonta

DURATION:
63.3 to 11.1 million years ago
Merycoidodontoidea

DURATION:  35 to 5 million years ago
Hyracodontidae

DURATION:  55.8 to 20 million years ago
Leptictidia

DURATION:  70 to 33 million years ago
Entelodontidae

DURATION:
37.2 to 16.3 million years ago
Amphiocyonidae

DURATION:
46.2 to 1.8 million years ago
Protoceratidae

DURATION:
46.2 to 4.9 million years ago
If all these numbers mean anything, it's that these groups had withstood millions of years of countless, various changes in their environments.  They had lived so long, yet despite their apparent flexibility, they tripped at the finish line.
The simple question is:  Why?

@JohnWDailey The questions is locked now, new comments are not possible any more. Please discuss this issue in the chat, the comments are not for extended discussion, so please stick to the rules.

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


text:
Effect of pH on protein solubilty and denaturation
I'm a little bit confused about the influence of pH on proteins.
Increasing or lowering the ph will give the protein a net positive or net negative charge, respectively. However a lower pH or higher pH will cause the protein to denaturate --> more hydrophobic amino acids will become free to interact between different proteins --> less solubilty.

let's clarify my question

take a look at the following figure:

this figure indicates that a lower or higher pH then the Pi will increae the protein solubility. However the Introduction to this article, for example, cites papers to support the following statement:

Changes in pH are shown to trigger formation of amyloid fibers and aggregation

the figure and the article are inconsistent in my opinion, so I'm definitly missing something. The first figure indicates that protein solubilty will increase when the pH becomes higher (then the pI). However the article statement indicates that an increase in pH will cause the proteins to aggregate, so lowering solubilty right?

http://biology.stackexchange.com/questions/43149/why-do-denatured-proteins-tend-to-be-less-soluble-than-the-native-protein

@akaDrHouse — Your reference is to a question to which there are no answers. This shows why people should not ignore the injunction not to use comments to provide answers. If you think the comment to that question is correct, feel free to copy and paste it as an answer. That is how StackExchange works.

My link had a comment that was correct.  A simple search in google reveals that denaturation of proteins often causes exposure of hydophobic regions, thus reducing solubility. @David perhaps that is why no more formal "answer" was needed. StackExchange also "works" to discourage one line answers, despite the fact they are often all that is needed.

@akaDrHouse Yes, denatured proteins are often less soluble because of the exposed hydrophobic inner residues. However, no one has yet made a connection between a pH change and denaturation. If you (or anyone else) can find evidence of that (it may exist, I just haven't searched), please make an answer.

@akaDrHouse — A search of Biology SE would list the previous question as unanswered. If someone chose to look at the question and read the comment they would have had no way of judging whether it was correct, as you assert, because it couldn't be voted up or down. There is a reason for the injunction you see when you open the comment box, and there is no excuse for ignoring it.

Sorry that my question was unclear, I clarified it and hope it's clear now @David

There is an everyday example that protein lose solubility on acidic pH... Milk+Acid--->Curdling. http://www.thekitchn.com/the-science-behind-why-acid-curdles-milk-222962

OK. Clarification fine. Have withdrawn my close vote and deleted my comment.

However, having looked at the paper you cite I have corrected your question. You say that the paper concluded the statement you cite. In fact the paper was about the correlation of pH optimum and stability in proteins and the citation is from the introduction and is only one of many examples given on the importance of pH for protein function.


text:
What are these bugs? [Image included]
Around August I started discovering these small critters throughout my apartment. They're around 0.5-1mm long, black with six legs and two stubby antennae. I keep my glasses on the floor by my bed when I sleep and every morning, they're are 5-8 of them crawling over my glasses. The same thing happens with my hat. A number of them have died on the window sill. What are they and what are the best ways of getting rid of them? (More pictures here: https://i.stack.imgur.com/pu6Bf.jpg)
Thanks!

I hope you have som pictures, it will be very hard otherwise!

I've attached one!

Good! Even though it's really hard to see. Looks like a beetle, at least. Strange that they are attracted to your glasses... Could you also add where you are located?

I'm guessing the glasses attraction is because of dried sweat on the bridge (my hat also has collected sweat over the years, though they favor one particular spot). I added a link to more images -- sorry they aren't high quality, the bugs are so small it's hard to get a good pic!  I'm in Chicago.

one of the picture you're linking to is a lot better than the others, maybe crop that and and add it here? anyway, i'm no expert, but some googling got me these that look kind of similar: http://puredefensepestsolutions.net/pest-solutions/pest-identifier/pantry-pests/merchant-grain-beetle/ but they (and other beetles like flour beetles) would probably prefer your kitchen. hmm...

(i keep commenting as i think of stuff) Do you have any food in your apartment? In that case I recommend that you go check that, in case they are breeding in your flour or something.

I appreciate all your comments and help! The merchant grain beetle does look like the ones I've seen. Most of my food out is dried (ie, pasta, unopened crackers). I haven't seen many bugs in the kitchen though I will be doing a thorough cleaning tonight!

It is one of the pantry pests and most likely a grain beetle. Check all dried foods in your cupboards. You cannot get rid of them until you locate the source


text:
Hair becoming white in one night after tremendous stress
You have surely heard about soldiers during the war whose hair became white in one night due to the tremendous stress.
I was wondering how is this possible biologically ?

Are there any documented medical cases of this? Without them, these stories are just hearsay. Stress does contribute to gray/white hair - just look at before and after pictures of the last 4 or 5 US presidents. However, this does not, and from a physiological perspective cannot happen overnight.

I've never heard of this phenomenon.

Seems Not at all a biological process; bcoz if it was due to solely biological effect (toxification, gene mutation etc) then only new portions of hairs would bleach. Bt since entire-hair bleached in 1 night; (as well hair is a dead structure); a biological-process-change has nothing to do on that older portion off hair. Sulphur Dioxide (SO2) has a bleaching effect. SO2 is produced from burning of gunpowders. maybe excessive smoke of gunpowder caused it; however bleach of SO2 is not persistent, so maybe some more complicated chemical reactions from warfare chemical-pollutants took place there.

@Chris Yes it is a completely a speculation and I'm transferring it as a comment. However I could not find any reference claiming change of hair color on warfare; however one of my school chemistry textbook says SO2 used in bleaching of gentle materials like wool, feather, silk etc.

The physiological condition you are looking for is commonly called Marie Antoinette Syndrome.
Under extreme psychological stress, the hair of the person does turn white but not in a single night (takes place slowly over successive days; in a matter of weeks) and cases of this has been reported worldwide generally in warzones.
Contrary to what you suggest, this phenomenon is extremely rare and I doubt many soldiers experience it.
Source- http://archderm.jamanetwork.com/mobile/article.aspx?articleid=712060
Another interesting tidbit the author mentions is whether Marie Antoinette herself suffered from it or not. The author goes in depth on the topic; regardless the syndrome is definitely real with documented cases. It is also known as canities subita.
Most in the scientific field now refer to it as an acute episode of diffuse alopecia areata. Alopecia areata is patchy hair-loss. This syndrome is referred to as such because the white hair eventually fall off.

Could you add a source to that?


text:
Gene vs. Protein Expression Assays
Are the terms gene expression assays and protein expression assays used interchangeably in molecular biology? Or is it expected of you to differentiate between the two terms.
For example, if I replace the DNA sequence of a gene of interest with the GFP DNA; and then subsequently quantify the fluorescence levels, am I measuring the gene expression of the gene of interest OR the protein expression?

Gene expression is the production of a functional gene product from a gene. So protein expression is a functional read-out of gene expression for gene loci that encode proteins.
However, gene expression is frequently, and erroneously, used to refer to measures of mRNA levels. The production of mRNA is a prerequisite step for the production of protein from a gene and it provides information about the transcriptional activity of a gene loci.
Translation of mRNA is a highly regulated process and
global assays highlight that mRNA transcript levels explain less than half of the variation in protein concentrations.

For example, if I replace the DNA sequence of a gene of interest with the GFP DNA; and then subsequently quantify the fluorescence levels, am I measuring the gene expression of the gene of interest OR the protein expression?

You are measuring both gene expression and protein expression from the promoter + GFP gene loci. If you are interested in transcription from the promoter then measuring transcript would provide a more direct measure.

Gene expression and protein expression are absolutely not the same thing. While counts of mRNA levels for a particular gene may give some indication of how much protein is present, many times it does not. Similarly, quantitating protein levels does not necessarily mean the relative levels of mRNA will be similar. There are many points for regulation between RNA polymerase rolling along the gene and creating the pre-mRNA and the protein coming out of the ribosome and being folded and transported to its correct place in the cell. mRNA can be silenced, degraded, or prevented from being translated by a number of mechanisms. Proteins themselves are subject to extensive regulation, with half-lives that can vary from seconds to weeks. Of course, genes are regulated in many different ways as well, from repressor proteins to methylated DNA to chemically-modified histones, and the number of polymerase complexes on the DNA and their relative transcription speed are also under regulatory control.

If I replace the DNA sequence of a gene of interest with the GFP DNA; and then subsequently quantify the fluorescence levels, am I measuring the gene expression of the gene of interest OR the protein expression?

You are quantifying the protein levels of GFP. mRNAs can be subject to sequence-specific regulation (such as siRNA), so you can't just say absolutely that GFP levels are equal to your gene product of interest. Many times they will be proportional, but some times they won't, so you'll need to do a number of other experiments to verify your results.


text:
Is there no such thing as species?
If you recreated intermediate species between every species on the evolutionary tree, would every species be able to reproduce with each other through a series of intermediates? Would this blur the concept of "species"?

Yes it is a concept like Fuzzy logic. It exists but its 'border' is not at all clear cut.

Like your head-hairs and beards can-not be distinguished with 1 clear-cut line; yet your head-hair and beard is not the same; they have some own features... beards grow-up only on and after adolescence.

'reproductive barrier' is a main, but not the only criterion to define a species.  It is used mostly for the animals. In case of other-kingdoms; only vegetatively reproducing strains, reproductive isolation could not be judged.  Rather we have to depend on other sorts of characteristics; from macroscopic through biochemical to molecular-genetic. In certain cases, especially for microbes, to define a species is really difficult; and sometimes instead species, directly the specimen-number ( like certain particular collection-number or culture number) is preferred.

Without need to recreate any species, https://en.wikipedia.org/wiki/Ring_species offers a real life examples of the situation proposed by the OP. It challenges the concept of species somehow, but also sheds light on the process of speciation.


text:
what is the ancestral relationship between dogs and cats and bears?
or Mr. person who may  have my answer,
     I would like to know the answer of my question so I can make a craft out of it and show my dog. I know it may sound silly, but biology is one of the very few things in science I'm good at, I would really like to know my answer when ever it is efficient with you.

Welcome to Biology.SE! Please take the tour. Your question needs some improvement to increase its chances of attracting a good answer. For instance, you should show that you've made an attempt at finding the answer yourself (for instance by Googling 'dog cat bear phylogeny' first and reading some of the links), and we don't need to know anything about your dog or your crafting intentions to answer the question :)

The same which is between you and your cat, and your dog and bear :P

@another'Homosapien' dogs, cats and bears are all Carnivora while humans are primates. So dogs and cats are more closely related than cats and humans are.

@Remi.b I ain't that good at classification. I just wanted to say that this would be the answer if you ask here without any research effort.

There are online resources such as tolweb.org or onezoom.org that allows you to visualize the tree of life.
Cats, dogs and bears are all Carnivora. The Most Recent Common Ancestor (MRCA) between dogs and bears lived about 44.9 Million years ago. The MRCA between the lineage giving rise to both dogs and bears and the lineage giving rise to cats lived about 51.4 millions years ago. You can find this ancestor here on onezoom.org.
Depending on your understanding of of phylogeny, you might want to have a look at Understanding Evolution > History of life, a short introductory series of slides, to understand the diversity of life and understand how to interpret phylogenies.


text:
How does hyperthyroidism cause diarrhea?
According to Robbin's Pathology, hyperthyroidism leads to an overactivity of the sympathetic system.
It also goes on to mention that this sympathetic hyperstimulation in the gut leads to increased motility leading to diarrhea and malabsorption.
How would sympathetic stimulation cause hypermotility? Isn't the parasympathetic system responsible for it?
Also, how does hyperthyroidism increase the sympathetic tone?

Can you please give a reference to the article?

@another'Homosapien' Its from Robbin's. A textbook for path.

Okay, I thought there would be an online version too...

https://studentconsult.inkling.com/store/book/robbins-cotran-pathologic-basis-disease-kumar-9/

Not that actually, I meant online version (PDF) of the book.

I believe these are the relevant pages (p.1083-1085) https://bit.ly/2C5Rdpu

Hyperthyroidism leads to an overactive sympathetic nervous system, hypermotility and diarrhea (Culp and Piziak 1986) (Geffner and Hershman 1992) (Maitra 2015, p. 1084) (Thomas et al. 1973). A demonstration of this is the patient presenting with the sole symptom of intractable diarrhea. It was found to be secondary to hyperthyroidism, and was treated successfully with β-adrenergic antagonists (Bricker et al. 2001).
Was the hypermotility due to excessive β-adrenergic activity, or insufficient α-adrenergic activity?
An article by Silva and Bianco (2008) states that β-receptor expression is under transcriptional control of a thyroid response element, and is upregulated by increased thyroid signalling. There is much less research on α-receptor expression, I would be much obliged if anyone can provide me with access to the following article:

*Bilezikian, JP, Loeb JN 1983, ‘The Influence of Hyperthyroidism and Hypothyroidism on α and β-Adrenergic Receptor Systems and Adrenergic
  Responsiveness’, Endocrine Reviews, vol. 4, no. 4, pp. 378-388.*

In any case, they add that increased β-receptor expression is rather modest, often overestimated, and cannot account for the magnitude of amplification in responsiveness induced by thyroid hormone (TH). Rather, thyroid signalling increases cAMP levels associated with a2 and β-receptors to a degree which could account for these changes.
Increased cAMP occurs during normal β-receptor function but is significantly potentiated by TH in several ways: increases in adenylyl cyclase; downregulation of β-receptor G-protein subunits, Gai and Gβ; and downregulation of phosphodiesterases which degrade cAMP. This explains the effectiveness of the β-adrenergic antagonist noted above, as propranolol decreases cAMP levels, thus decreasing hypersensitivity of the hyperproliferated β-receptor (Silva and Bianco 2008).

“The reduction of the sympathetic activity associated with
  hyperthyroidism outflow (via increased rate of norepinephrine
  metabolism to decrease overall levels) is likely overridden by the
  increased sensitivity, as suggested by the clinically significant
  amelioration of the adrenergic symptoms with β-adrenergic blockage and
  the consistent observation of elevated cAMP production.” (Silva and
  Bianco 2008).

What are the effects of preferential/hyperactive β-receptor function on gastrointestinal motility?
The β1-receptor increases ghrelin secretion from the stomach – a peptide secreted when the stomach is empty to increase hunger, increase gastric acid secretion and gastrointestinal motility. The β2-receptor promotes smooth muscle relaxation (decreased GI motility) but contracts sphincters of the GI tract (Adrenergic receptor 2018).
β-adrenergics also promote the secretion of gastrin – a peptide which increases antral muscle mobility and promotes stomach contractions; relaxes the pyloric sphincter, which increases the rate of gastric emptying; is involved in the relaxation of the ileocecal valve; induces pancreatic secretions and gallbladder emptying; and contributes to the gastrocolic reflex (Gastrin 2018) (Katzung and Trevor 2014, p. 143-144).
What are the effects of relative α-receptor deficiency on gastrointestinal motility?
Considering that β-receptor antagonism causes a relative increase in α-receptor activation we should consider them also. The α1-receptor causes smooth muscle contraction. The α2-receptor causes negative feedback on norepinephrine signalling, relaxes the gastrointestinal tract when activated on presynaptic terminals and contracts of sphincters in the GI tract. It does this by decreasing levels of cAMP (whereas β-receptors work by increasing cAMP) and so it will become less active as TH becomes more active (Adrenergic receptor 2018) (Silva and Bianco 2008).

What are the adrenergic-mediated effects of hyperthyroidism on gastrointestinal motility?
Under prolonged conditions of excess TH overall peristalsis will
increase due to mixed effects on smooth muscle contraction primarily
via α1, and β2. There will be an increase in hunger and gastric acid
  secretion via ghrelin (Adrenergic receptor 2018). Hyperphagia and
hypermotility are both suggested to play a part in steatorrhea
  (Culp and Piziak 1986).

How does hypermotility cause diarrhoea?
In addition to the mechanisms above, it has also been suggested that excessive fatty food intake contributes to the steatorrhea seen in patients with hyperthyroidism. This is compounded by a reduction in time that digestive secretions can act on chyme, ultimately leading to a reduction in absorption and an increased liquidity of the stool (R Santra, Calcutta School of Tropical Medicine, 2016).
Finally, it is important to note at this point that not everyone with hyperthyroidism will show hypermotility - some hyperthyroid patients show delayed gastric emptying (Pustorino et al. 2004). Indeed, constipation has been reported in patients with hyperthyroidism (Culp and Piziak 1986). Nonetheless, it is held that dysthyroidisms alter the motility of the gastrointestinal tract, and we do not completely understand how this works (Pustorino et al. 2004).

References to come, if desired.

search that article at gen.lib.rus.ec ,its there


text:
What´s the role or function of the homologous arms in a donor template in a knockout/knock edition via Crispr-cas9?
I have to make an exposition in my university about Crispr-cas9 edition and I have some questions about the method. In the knock out/knock in technique is used a plasmid containing the DNA that codifies for the Cas9 protein and guideRNA and a Donor template that has a gene for puromicine resistance, and a DNA that codifies for a fluorescent protein and "left homologous arm" and "right homologous arms". My questions is What's the fuction of the homologous arms?Furthermore what's the role of the Loxp(look at the image)?
The method is described here   http://www.origene.com/assets/documents/CRISPR-CAS9/CRISPR_manual.pdf   (page 5-10)

This is not the CrispR/Cas9 system but the LoxP system which works differently.

It is there to facilitate homologous recombination and thereby a knock-in. See http://biology.stackexchange.com/q/29735/3340

@ Chris This plasmid can be part of the CRISPR based knock outs, the LoxP sites are there to recycle the marker if you want to do successive knock outs


text:
Are there public records of results with laetrile treatment against cancer?
I'm looking for what the title says. This is based on the book by Edward Griffins. Is laetrile actually fatal because of its cyanide content? Or can it really help in this fight?

Yes, there are several articles describing experimental data from animals and clinical trials in humans. The results clearly show that laetrile is not effective for cancer treatment, and the drive for laetrile as a cancer drug is widely considered to be a quack. See for example this NCI summary or this article.
Laetrile is a modified form of Amygdalin, a toxic plant product found in some seeds and nuts, for example bitter almonds. The compound contains a cyanide moiety and can cause cyanide poisoning. It was labeled "Vitamin B17" by Ernst Krebs in an attempt to get the compound classified as a nutritional supplement rather than a pharmaceutial (to escape FDA regulations), but this is misleading; it is not a vitamin.


text:
How are antibodies extracted from donor blood?
When blood is donated, the antibodies within it are extracted, but how exactly do they do it? How do they take out the antibodies within the blood, what process do they go through?

Do you have a source that the antibodies are removed?

Just look at it, if they didn't remove the donor's antibodies only people with the same blood types could donate. If the antibodies weren't taken out for example type O wouldn't be a universal donor. O has A and B antibodies so it wouldn't be compatible with any other types. In order for it to be the universal donor(which it is) the antibodies of the donor blood must be removed. It's also common knowledge, but here is the logical explanation for Chris.

This is the reason why O- (universal donor) is so much sought after. And why blood for some blood groups is easier available (A + for example) than for others. Oh, and belittling other users is always a bad idea since you want something. There is no obligation to write an answer, though.

I am really sorry Chris if you thought I was belittling you. I didn't see my answer having an offensive tone, sorry if it did. I was just trying to answer your question so if others stumble upon this and have the same question the answer would be present.

I don't believe they do remove the antibodies but rather they match and screen the donor antigen and antibody profiles to those of the recipient. The process is very briefly outlined on the Red Cross website;

Most blood is spun in centrifuges to separate the transfusable components – red cells, platelets, and plasma

The primary components like plasma, can be further manufactured into components such as cryoprecipitate

Red cells are then leuko-reduced

Single donor platelets are leukoreduced and bacterially tested.

The article in wikipedia explains the screening for blood transfusions;

Patients should ideally receive their own blood or type-specific blood products to minimize the chance of a transfusion reaction. Risks can be further reduced by cross-matching blood, but this may be skipped when blood is required for an emergency. Cross-matching involves mixing a sample of the recipient's serum with a sample of the donor's red blood cells and checking if the mixture agglutinates, or forms clumps. If agglutination is not obvious by direct vision, blood bank technicians usually check for agglutination with a microscope. If agglutination occurs, that particular donor's blood cannot be transfused to that particular recipient.

Thanks Michael_A, if you have time to answer a follow up question here it is. Are all the antibodies and antigens in the centrifuged blood removed or do some necessary antibodies get transferred to the patient.

@genius Antibodies are not removed by centrifugation - they stay in solution. When you spin so high, that antibodies precipitate, all the cellular components of the blood will not survive this.

I believe the antibodies are predominantly in the plasma component. Cross-matching donor and recipient blood tests for the presence of problematic antigen-antibody interactions.


text:
What is considered incorrect for a cladogram's time axis?
I am looking for help (and possibly references) regarding the correct mapping of time in a cladogram. As far as I know, it is considered incorrect to draw a time axis diagonally in a cladogram as shown below:

This setting would lead to conclusions like: Species B and ancestor b lived at the same time, because they would both fall upon the same place on the time axis. But we know this is incorrect. Or is this an acceptable positioning for a time axis?
The image below correctly represents the time axis, if I'm not wrong, using a vertical axis.

This positioning makes it clear that species B and b are not living at the same time. In this case, species B is alive and b is an extinct ancestor.

I think it really depends what you're trying to show. The folks in our lab that do these sort of diagrams make scaled cladograms for time (calculated by rates of mutation).

@James does your comment imply that the first diagram could make sense in some circumstance? Following, the OP's description I don't understand how the first diagram could make any sense.

Why did the question receive two close votes?

@James I am sorry, but I don't really understand your comment. I don't think it makes any difference what one is trying to show with the cladogram. A correct time axis shouldn't depend on the information being presented. The branch lenghts would matter in a phylogram, but that's not the case here.

@Remi.b I voted to close because OP introduced a cladogram I have never seen before that is wrong and tells us why it's wrong. My comment was trying to explain that even the figure 2 axis has problems. For example is  A as genetically distinct from a as D is from a, or is it just reflecting time passed? I'm not entirely sure what the question is... Figure 2 is better than Figure 1, but it's still arguably incorrect depending on what you want to show.

@James The quantitative diagrams made in your lab are certainly more precise and more useful to evolutionary biologists. But qualitative ones such as the OP seems interested in are very useful in the classroom and are commonly found in textbooks. In this capacity they generally refer to higher groupings than species. Example, in reference to OPs diagram: A = bryophytes, B = ferns, C = gymnosperms, D = angiosperms.

In your first example, each species becomes "frozen in time" once it evolves implying there is no further change. A slightly more complex cladogram will help.

Imagine the species A ancestor, after branching off the remote ancestor, serves as the ancestor to species E. You need to draw that line in some direction other than along A. Most popularily, that line would extend upward to the right. With the temporal axis as you first show, how did species E even evolve since A is frozen in time? Furthermore, the advantage of a vertical time axis allows us to see that species E appeared after species B and a bit before species C (horizontal dashed line).

Thanks for your answer. That's precisely my line of thought as to why the first setting is wrong. I guess the person I'm trying to convince is connecting the nodes and ancestors to the time axis horizontally, instead of using a line perpendicular/normal to the axis. That's why this person said the first option is not wrong.


text:
Can "red" cone cells actually see much red light?
In electronics, the most common color scheme is the "red-green-blue" (RGB) scheme.  This choice is often justified by claiming that the long-  (L), medium-  (M), and short- (S) type cones in the human eye are most sensitive to red, green, and blue light respectively.  But this seems clearly wrong if you look at the actual normalized frequency receptivity spectra for the three types of cone cells:

It's clear that the L-type cones are actually most sensitive to yellow-green light and are actually relatively insensitive to red light. (Presumably the brain distinguishes between yellow, orange, and red light by the rapidly decreasing ratios of M-type to L-type signal.)
My question is threefold:
(1) The L-type cones are usually called "red" cones.  Is this simply incorrect, or is there some justification for this name that I can't see from the receptivity spectra?
(2) Does the RGB color scheme give a better color range than, say, a "yellow-green-blue" scheme (which would more closely correspond to the actual cone sensitivities) simply because red is at one end of the visible spectrum, so you can more easily get a wide color range?
(3) If this is the case, do we not use a "red-green-violet" color scheme (which would give an even wider color range) simply because the human eye is so much more sensitive to blue than to violet light?

Wonderful question. Thank you. But I think you could include that curve (Red with a bump at violet region) into question... that would not take much place. You could use small-sized version of it. I uploaded a smaller version of it (https://i.stack.imgur.com/qjh6O.png). You could use that also.

The same question can be asked about the color filter arrays in front of digital camera sensors. Though the "red" filter is usually most transmissive to light at around 595-600 nm (and thus "red" filtered pixels are most sensitive at 595-600 nm), every drawing you see of them anywhere, even in highly technical scientific papers, illustrates them with 640 nm "Red". Why are Red, Green, and Blue the primary colors of light?

This is a good question. The first  thing to note is that human colour vision is very complex and still poorly understood. If you visit the wikipedia page on RGB,  you will find that this correctly mentions that the S, M and L cones are most responsive to violet, green and yellow wavelengths respectively (which answers your first question - calling the cones red, green and blue is primarily for historical reasons, because there aren't any real wavelengths that only activate a single cone, it's hard to say what colour a cone 'is'). So why do we use red, green and blue phosphors? A practical answer can be found by looking at the CIE 1931 colour space: this was essentially an attempt to find how one could add together different amounts of a small number of wavelengths to make the result indistinguishable from any desired wavelength (read the linked page if you want more information, also have a look here). The result found was that the colour matching functions should look like the following graph (what this is showing is how much of a red, green and blue light are required to simulate a wavelength):

You can see that this is similar to the responses of the cones except for the peak in the red (which corresponds to violet looking like red-blue):

To answer the question in your title, red cells do see the most red light of any cone, but that is not where they see the most light. Here is an example set of spectra of the red, green and blue phosphors in a CRT:

To answer your question about why we use red, green and blue in the first place (rather than yellow-green-blue or red-green-violet), it's good to understand why the CIE 1931 functions are that shape in the first place. The wikipedia RGB page mentions that:

...good primaries are stimuli that maximize the difference between the responses of the cone cells of the human retina to light of different wavelengths, and that thereby make a large color triangle.

This gets at the fundamental reason, which is that it is generally believed that we do not perceive colours in terms of the activities of each cone, but in terms of the differences between those signals (as it says here), an opponent process. The following image illustrates a simplified version of how the opponent signals in colour vision processing are thought to function, so that the resulting signals are a black-white, a yellow-blue and a red-green axis:

This image shows the theorized shapes of the response curves of these opponent functions (see here for an interesting historical paper on this theory and here for more details and some predictions of the theory):

It is possibly apparent from the last graph why the CIE 1931 colour graph is the shape that it is, since we see red as a bimodal distribution with a distribution of green in between, and a large distribution of blue at short wavelengths and yellow is red + green. (Incidentally this also explains why we also perceive yellow as a primary colour - see the 4 highlighted points R, Y, G and B where one curve passes through 0). Additional information on the neurological and psychological correlates of colour vision can be found here and here and more technical theoretical details here.
The upshot of all of this is that red, green and blue are the best 3 colours to use as the basis for additive colour mixing, but not because they are what L, M and S cones are most sensitive to. Rather it is because it has been shown that these particular colours fall where there is maximal difference between the cone signals and because they can accurately represent all of the colours in our colour space as illustrated by CIE 1931 (due to being widely spaced and all perceived easily as you have mentioned in points 2 and 3 of your question). Effectively, the reasons are complicated and to do with the neurological processing of the colour signals and the differences between the signals rather than the straightforward signals themselves.

I think it is pretty interesting. What I thought what was most interesting about it was the way it explains why we see yellow as a primary colour too (where the curves cross zero).

Approaching this as a knowledgeable artist and designer who also understands about trichromatic colour vision, I see that the answer above is a good one - but scientists often have an overly complex way of explaining things. I would have put it in the following terms. As the first graph above shows, most wavelengths stimulate two or three of our cones to some degree. As the scientific answer above says, the best primary colours are those that give the greatest colour separation/distinction. Therefore, it makes sense to take the first primary as RED, defined as the colour that can ONLY be seen by the red cone (the blue and green cones are insensitive at the longwave end of the visible spectrum); as seen in the second diagram, this is from 650 nm upwards. It also makes sense to take the second primary as BLUE/VIOLET, defined as the colour that can ONLY be seen by the blue/violet cone, which occurs at the shortwave end of the spectrum, around 400 nm. Finally, you need to choose GREEN, which is the colour that, by definition, is NEITHER blue/violet NOR red (neither of which contain green) - the middle colour. Note that although red has no green, green does contain red, as we perceive it with both the green (M) and red (L) cones. The above three choices give the best separation. Green is at its most distinctive at about 546 nm where the blue cone loses most of its sensitivity.
My final point is about violet. Colour theories always assert that 1) violet is the same as indigo or dark blue, and 2) purple is not violet and is not in the spectrum (a 'fact' shown in the CIE chart). My eyes tell me that both these assertions are untrue. The colour violet is, to my eyes, a bright vibrant hue that many people also refer to as 'purple' and which patently IS in the spectrum; I see it in every rainbow. It is clear to me that I, along with all the other people who see colour as I do, perceive more sensitively at the shortwave end of the spectrum than the textbooks would have us believe.
I have been doing research on this for some years, which I hope eventually to publish, but I conjecture this is a side effect of being a carrier of the gene for deuteranomaly (a type of R-G colourblindness) which applies only to women (hence the fact it tends to be women who get enthusiastic about bright violets and magentas).
So in my opinion (and according to my ongoing researches), the correct primary colours are RGV - red, green and violet.
The deuteranomaly gene has also been found, in one case, to confer perception of a fourth primary colour in the yellow-orange area of the spectrum (Study by Jordan, Deeb, Bosten and Mollon, 2010; https://doi.org/10.1167/10.8.12) so it could be that for some carriers of deuteranomaly the primary colours are actually RYGV and this is a further theme of my research. Please contact me if you want to work with me on it - rahbeckett@gmail.com.

Welcome Rachel. Please take our [tour] and refer to the [help] for guidance. Could we prevail on you to [edit] some paragraphs into your post, at present it's a bit of an unreadable wall-of-text. Anyhow, enjoy the site.

In regards to your comments about violet - the fundamental difference between violet and purple is that the former is a spectral colour, which can be elicited by monochromatic light, whereas purple usually refers to mixtures of red and blue. Thus any 'violet' displayed by a computer screen is technically a purple. The generally accepted reason for this is the slightly increased differential activation of the 'red' cones by short-wavelength light. Nevertheless you are right that perceptually they may be indistinguishable in some cases.

Also, as I mentioned in my answer, the fact that we perceive yellow as a fourth perceptual primary colour (along with red, green, and blue) is explained by the opponent process colour theory.


text:
To what extent is excretory control a learned vs. instinctive behavior?
Human babies are clearly not born knowing whether/how to hold in urine and feces, and teaching them to do so requires a nontrivial (really nontrivial...) amount of work on the parents' part.  But once this skill is learned, it becomes so effortless that one does it automatically in one's sleep.  I can't think of any other learned behaviors that are either (a) performed while unconscious, or (b) controlled by the parasympathetic nervous system, both of which are true for excretory control.  The fact that, once learned, excretory control becomes so "automatic" seems to suggest to me that it's not entirely a learned behavior.  If no one ever actively taught a baby to control its bladder and bowels, would it eventually learn to do so on its own (suggesting that excretory control is actually an instinctive rather than learned behavior)?  Presumably this experiment has never been performed on a human baby, but are non-human animals born knowing how to control their bladder and bowels, or is this a learned behavior?


text:
Evolutionary advantage of F plasmid in bacterial conjugation
Hi I would like to ask a question on bacterial DNA exchange, namely conjugation via F plasmid. It seems to me that all the F plasmid codes for is the sex pilus. What is the evolutionary advantage of the F plasmid? Does it code for anti-biotic resistance as well? Or enhances binary fission for reproductive success? Also, if conjugation transfers duplicated F plasmid from a F+ cell to an F- cell, why aren't all bacteria cells (that are capable of being F+/-) already F+? Is there a mechanism that somehow degrades your F plasmid?
Thank you in advance! I couldn't find the answers anywhere online.

F plasmids allow for the genetic exchange of material between cells, it's the closest thing to sex for most bacteria. Parts of the F plasmid are homologous to the chromosome of E. coli (mainly the transposons present on the plasmid) and through homologous recombination they can pick up bits of the chromosome. A lot of studies have been done where bacteria acquire traits such as galactose or lactose utilisation through these genetic exchange. They therefore allow fitness enhancing DNA to spread quickly through a population or species barriers [Ref].
Antibiotic resistance is not carried on F plasmids but there are many conjugative plasmids that do carry resistance genes (R plasmids). The F plasmid does carry a toxin/antitoxin system (ccdB/ccdA) [Ref]. If the cell loses the plasmid it will not be able to replicate its DNA because the toxin protein is very stable while the anti-toxin is rapidly degraded. So besides the evolutionary advantage there is also the possibility that it is simply 'selfish DNA' (see Richard Dawkins the Selfish Gene for details on this).
There are certain circumstances under which the F plasmid does not transfer such as low temperature so it is possible for a bacterium to lose the F plasmid and not get it back by conjugation. Maintaining a relatively 'useless' piece of DNA does have its metabolic cost so loss might confer a growth advantage.

Seems like the F plasmid would be more of a burden than anything.  Perhaps its just a selfish epitope.  Seems comparable to a parasite.  Maybe its a disadvantage to the individual, but an advantage to the bacterial strain due to recombinants generated through transfer of chromosome in Hfr cells.


text:
Depositing/publishing protein structure simulations
Just wondering if anyone has any information on what the general consensus on publishing/depositing online protein structure simulations is?
I've been doing a fair bit of work to characterise the 'quality' of the simulations I have (how well they approximate known homologous structures), but don't know what is generally thought of protein structure simulation methods. They do a lot of work in the CASP programs every couple of years to assess whether they simulate accurately, so a plausible structure simulation should be a valid surrogate for an otherwise unknown protein IMO?
Are the online databases purely for structures resolved experimentally?

The consensus is "not publishing/depositing anything". Reproducability might be an issue throughout biology, but it's sad to see that in the one area that should be perfectly reproducable every time the standards are as low as they are. Please just put it somewhere, supplementary info or any kind of database is better than nothing.

Yeah I fear you're right...read a paper recently about the number of genomes that go unpublished...and my group is as guilty of that as any. They will be included in my thesis certainly, and can be made available through our HPC infrastructure. Really I was just wondering if you tried to publish a paper with simulated rather than experimented structures, whether you'd be opening yourself up to serious criticism...

I published a protein engineering paper based on a model structure. I regret that we didn't publish the structure of the model (although it was just made with YASARA standard settings, nothing special). We had some troubles publishing it where we wanted, but using the model as the basis for protein engineering was never an issue.