reproduction - Cytoplasmic determinants - protostomes and deuterostomes

The two distinct types you have mentioned in your question (determinate/indeterminate cleavage) are actually called autonomous specification and conditional specification, respectively.

In the case of the former one, if we were to remove a blastomere, it would still produce the previously determined type of cells, while in the case of conditional specification the cells, which are going to be produced, depend entirely on the neighbouring ones. The latter's ability to alter their fate is called regulation.

As for answering your questions, cytoplasmic determinants are spread unevenly in deuterostomes as well, as otherwise no axis could be developed.

You might be interested about this answer as well.

I've used the following book as source: Gilbert, S. (2000). Developmental Biology [ online version ]

genetics - What is the frequency of double-hets between parent and child?

Say both parent and child are genotyped for all SNPs. In this setup we are only looking at variant positions between one parent and child - so neither parent nor child are homozygous reference (no AA/AA) in the millions of positions we are studying.

Assume all variants are biallelic and there is no de novo mutation (no AA/BB or BB/AA)

P    C
AA   AB
AB   AA
AB   AB
AB   BB
BB   AB
BB   BB

What is the fraction of AB/AB among these possibilites?

We are looking at all positions in the genome so the minor allele frequency (MAF) of B allele varies. You can choose whatever B frequency you like.

Atomic force microscopy: depth penetration?

Taken right from the Wiki page you linked to:

AFM only images the surface of a specimen, to a maximum depth of 10-20 µm and a maximum scan area of 150 µm x 150 µm. Compared with scanning electron microscopy, SEM has a much larger depth of penetration and scanning area (~1 order of magnitude greater). AFM is also a much slower scanning method.

senescence - Telomere elongation methods?

What sort of telomere elongation methods are there currently?

Would this stop aging? (edit: No, probably)

I couldn't turn up anything good on google. I was thinking that maybe you could sequence the telomeres, trim them all at a certain point, and then engineer a polymerase molecule to extend from that same point. Is this how it's done?

What is the difference between vegetable and fruit?

A true fruit is a ripened ovary that usually starts ripening when it is fertilized. And vegetable is any vegetative part of the plant which is edible and contains stored food probably in the form of starch.
These definitions are not exact as there are a lot of fruits which are fruits but do not strictly follow the given definition. See Syconus, Composite fruits, Sorosis.etc

Classification is based on several different criteria, for example the mode of reproduction, arrangement and design of flowering parts and flowers and also on the basis of habitat and habit.

biochemistry - Is breathing in deodorant fumes dangerous for my brain?

You can definitely absorb alcohols by breathing them in. But doing do is far less efficient than drinking alcohol, so you don't have anything to worry about on that front.

To address your concern we have to answer two questions: how much alcohol is transfered per unit time and is there a local dosing effect due to proximity to the blood brain barrier.

It is probably pretty obvious that while alcohol evaporates rapidly compared to water, it still takes quite awhile. Imagine trying to inhale a glass of whiskey. You would get a serious headache but 30 minutes in you would still have an almost full glass of whiskey and no alcohol buzz. For an amusing anecdote relating how hard it is to get drunk off of inhaling even from a machine designed for it, see here

As to the second point - Fortunately, the blood brain barrier is a two way street for alcohol, which means that you can't get drunk in your brain if you don't have high levels of alcohol in your bloodstream. The two would dialyze into a reasonably balanced equilibrium.

bioinformatics - What percentage of protein isoforms have different functions?

I am looking for studies on how many protein isoforms have different functions, preferably in human. We know that a great many, if not most, of human genes are alternatively spliced and that many produce different protein isoforms. Has anyone looked at how many of these isoforms have different cellular functions? If someone could point me to a published paper, that would be great.

If no such study has been made, can anyone recommend a database from which this information could be extracted? GeneOntology is gene based so the information cannot be found there. Genes will be annotated to specific terms, not their protein isoforms. Also, I would need to be able to do this in a high throughput manner, I am not interested in specific proteins but in what percentage of all isoforms have different functions.

Ideally, I would like to be able to extract, for every human gene, the list of the different protein isoforms it encodes and whether their functions differ, or at least what those functions are.

human biology - Is the eyes' movement discrete?

When tired and it was dark, I noticed that if I focused on a dim light source and moved my eyes fairly rapidly sideways, the resulting images that lingered for a short while were not smoothly blurred together, but were discrete.

I assume this is not due to the brain's inability to process the data fast enough or the retinas not repairing fast enough when light breaks part of them down, so I am lead to the conclusion that eyes (if not generally, sometimes) move in very small sudden jolts rather than smoothly.

Is this correct? What is the reason for this (is it due to the eye muscles being unable to sustain motion for a long time, or something to do with the mechanics of the eye)? Was this result anomalous?

human biology - Is diabetes mellitus a sex-linked disease?

Is either of them a sex linked disease? Can either one be inherited? My book says, "this disease is transmitted as a recessive genetic characteristic." What does this mean?

Neither are sex-linked. Type 1 can be directly inherited (in a non-Mendelian fashion), but Type 2 genetic factors mostly increase risks. "Recessive genetic traits" are traits that only express themselves when ONLY the recessive alleles are present in the organism (a dominant allele, if present, will 'overpower' recessive one).

Longer info:

Diabetes mellitus Type 1 (Juvenile Diabetes) is inherited, but it is autosomal with complex dominant/recessive rules:

Type 1 diabetes is a polygenic disease, meaning many different genes contribute to its onset. Depending on locus or combination of loci, it can be dominant, recessive, or somewhere in between.

That results in some interesting, albeit complex, expressions:

The risk of a child developing type 1 diabetes is about 10% if the father has it, about 10% if a sibling has it, about 4% if the mother has type 1 diabetes and was aged 25 or younger when the child was born, and about 1% if the mother was over 25 years old when the child was born.

Diabetes mellitus Type 2 does have genetic components, but the vast majority merely increase the risk of developing Type 2 Diabetes. Environmental factors play a large role in Type 2.

Excess body fat is associated with 30% of cases in those of Chinese and Japanese descent, 60-80% of cases in those of European and African descent, and 100% of Pima Indians and Pacific Islanders.

taxonomy - An unexpected mushroom in my garden

My grandma is a great fan of mushrooms and knows quite a lot about them. About 10 years ago, she started throwing out mushroom remnants in one special place, in order to grow her own mushrooms. In fact, for last three years we found some parasol mushrooms (Macrolepiota procera).

Today she found something, that nobody at home can classify. From what I searched, it might be Cortinarius privignoides, but it is marked as almost extinct here in Poland, so I doubt this classification. Maybe you have seen this or know what it really is:

The hat is light brown with faint violet shades, the leg on the outside is partly violet too, but the inside is all white.

Some more photos:

All three

The gills are lighter brown, also with a violet tone

The cut through the leg

The cut through the hat

At my parents' house I found one more mushroom atlas, and a new candidate: Cortinarius traganus, but one thing is not right - the ones that I have don't have a smell and gassy webcap should smell and taste bad.

neuroscience - Which Receptors are Involved in the antidepressant effects of SSRIs?

You're right, those are all important! There are several good reviews on the mechanism of action antidepressants. I like Molecular Pharmacology, by Nestler, or even Principles of Neural Science, by Kandel. I think a textbook is going to be your best bet, in terms of getting up to speed here, as this is largely an already-researched issue, but here are some good review articles as well:

1. Bonhomme et al., 1988


2. Charney et al., 1981


3. Norbert & Esposito, 1998


4. Spencer, 2012

If you have a more specific question, let me know!

genetics - Phenotypic Variation of cattle - looking for academic sources

Can someone please point me in the direction of a good academic article on the following:

What are possible sources of phenotypic variation of different 400 day weights of cattle?

Furthermore how much variation is likely to be due to each contributing source?

I have tried the following searches in google scholar:

• Phenotypic, genetic, environmental cattle weight


• Phenotypic variation cattle weight


• Phenotypic variation


• Phenotypic variation, genetic


• genetic variation, dam, sire

human anatomy - What negative effects can pinhole glasses have on the body?

Probably not many side effects except in specific instances, but no benefits either. My guess is that there are potential side effects because these glasses reduce the amount of light that the eye receives and restrict the visual field. Therefore, the restricted visual field would be bad for activities such as driving, in which you need your peripheral vision. And the reduced light makes objects appear dimmer, so it is harder to see with them at night. I also imagine (just a guess) that they would be bad for very young infants, who are almost always born without perfect vision and require some visual stimulation to correct.

There are probably many reasons why optometrists use a pinhole occluder for diagnostic purposes, but never prescribe it as treatment...

evolution - Why are urban birds still scared of humans?

Perhaps counter-intuitively, fear of humans is often a learned behaviour. There are accounts, such as one made by Charles Darwin following his visit to the Galapagos islands;

In Charles Island, which had then been colonized about six years, I saw a boy sitting by a well with a switch in his hand, with which he killed the doves and finches as they came to drink. He had already procured a little heap of them for his dinner, and he said that he had constantly been in the habit of waiting by this well for the same purpose. It would appear that the birds of this archipelago, not having as yet learnt that man is a more dangerous animal than the tortoise or the Amblyrhynchus, disregard him, in the same manner as in England shy birds, such as magpies, disregard the cows and horses grazing in our fields.

From "The Voyage of the Beagle" - http://www.ling.upenn.edu/courses/hum100/Beagle17.html

Birds born and bred in proximity to humans will have learned that we are actually to be avoided.

Ducks and swans, for instance, (and this is quite anecdotal) live in very close proximity to a lot of humans in cities, and feel confident walking picking up food. However if you try to get close to one they are very quick to get out of the way. The only exceptions to this are learned behaviours, such as when someone stands and feeds them.

In the wild animals may be cautious of humans if we are much bigger than them, but if they have no experience at all of human contact they may just ignore them. This quite often happens with film crews in Antarctica, as in the below image from the BBC's Frozen Planet series.

nutrition - Has there ever been an attempt to create nutritionally tailored food for adult human consumption?

Shortest answer: there's nothing special in human biology, you could totally make it

Short answer: Bachelor chow!

I would totally buy this stuff if they made it. The closest I have now to bland, flavorless, zero thought/effort food is Wheaties.

longer answer:
Seriously though, dogfood for humans wouldn't be that hard to make. If you just took everything from the RDI guidelines (the Recommended Daily Intake from which they calculate the percentages you find on food labels) and mashed it all together into a thick brown paste you would get all of the macro and micro nutrients that you theoretically require. Precise proportions are irrelevant because:

a) everyone is a little different, and

b) to some extent, our bodies are able to fine tune our digestive tracts to fit our specific diets (presumably this tuning would occur even faster if you ate the exact same thing for every meal). You're a mammalian omnivore. Enjoy it!

You probably shouldn't try to live on something like this for the rest of your life, since there's plenty of research suggesting that there are other micronutrients, such as phytocompounds (i.e. plant stuffs), that are poorly understood but may be beneficial to humans. One thing to note here is that any health claims about any antioxidant that is not on the list of essential vitamins (vitamin C is an antioxidant on the list) are almost certainly bunk and/or hokum.

The upshot is that you would only need, at most, utterly minuscule quantities of these miscellaneous micronutrients. You would be fine(ish) for at least a few months. For related reasons, your statement:

The composition is also known for human babies. This is manufactured as "baby formula". Everything baby's organism needs to be healthy (and to grow).

is largely correct but somewhat flawed. While it is true that many babies are raised solely on formula and subsequently turn out just fine, there are some things that you can only get from mother's milk. For example, the mother passes on components of her own immune system to her baby through her milk, which then help to strengthen the baby's own immune system. These are the kind of subtle but useful compounds which are encountered in a "natural" diet but which could never realistically be included in people chow.

evolution - Is there variation of AT/CG ratio along species?

That ratio is essentially, as WYSIWYG pointed out, called GC-content. In actuality, GC-content is reported as $(G+C)/(A+C+G+T)$, converted to percent; i.e., what percent of the genome is G or C.

There is vast variation in GC-content, both amongst species and within a given species' own genome. For example, in humans the first intron and exon are generally more GC-rich than following introns/exons.¹ Genes themselves are often found in higher GC areas,^2,11 in particular CpG islands are found near a large number of (mammalian) promoters.³

Across species, there can be a big difference. Yeast and Arabidopsis are both around 35%^4,5 whereas Plasmodium falciparum is around 24%;⁶Carsonella are even lower, at around 16.5%.¹⁴ On the other hand, the plankton Emiliania huxleyi is around 65%⁷. We can use these differences to study genomic history. Bacteria often have genes from all over the place thanks to horizontal gene transfer, and GC-content can be used to differentiate between their own genes and those from horizontal gene transfer;⁸ a good example is the CRISPR-Cas system,⁹ even in a virus!¹⁰

Here's a list of a few things genomic GC-content is correlated with:¹⁵

• genome size


• whether the bacterium is free-living or not


• the environment


• aerobiosis


• nitrogen utilization

In the lab, high GC-content often means a harder region to work with, as the presence of three instead of two bonds (between A and T) requires more energy to break;¹² anything involving primers can be made more annoying, including (especially, to some) sequencing. There is a theory that high GC-content would be an adaptation to high temperatures, to avoid DNA damage, but that is controversial.^13,16,17,18

speculative - Why Didn't Evolution Cause the Human Body to become Streamlined?

If streamlining makes movement/locomotion quicker and easier, why didn't the apes evolve into life-forms that had streamlined bodies (much like fish)?

As with everything in Evolutionary Biology, you must ask yourself: Gain vs. Cost?

In your specific case, the Gain is very little. Air isn't nearly as dense as water, so a streamlined form won't show a major benefit unless the organism is traveling very, very quickly. This is why you see it in birds; raptors can travel over 100mph while diving, and at those speeds small changes in drag can mean the difference between dinner and starving. Smaller birds often make very quick turnabouts and changes in direction mid-flight where, again, small changes in efficiency can mean the difference between life and death. The cost was is worth it.

For apes and monkeys, moving very quickly isn't a case of living or dying. That's what we evolved opposable thumbs and prehensile feet(/tails) for. You don't need to run fast when you can climb a tree and simply get away from any predators on the ground. After we came down from the trees permanently, our larger brains allowed us to use tools to fend off predators - which, again, is much simpler than evolving an aerodynamic form that won't make a difference until you're running at the speed of a car.

So, in lieu of becoming a land-shark, we have hands that can use keyboards and minds that can invent the keyboard. Unfortunately, while the gains are many, the costs do include both a very long period of time where humans are helpless without parents, and an absolutely terrible form of locomotion with our upright stance on forward-pointing knees. Though you won't catch Cheetahs digging sewers anytime soon.

neuroscience - How does a pinched nerve cause pain (at the molecular level)?

As AndroidPenguin described the nociceptive pathways are activated by inflammation or noxious chemicals.

Sometimes pain can arise independent of active nociceptive pathways. Most evident in cases of Neuralgia and perhaps in case of Pseudoneuromas.

In certain cases the injured nerve causes disinhibition of the pain pathways arising from the dorsal horn of spinal cord. This disinhibition is because of loss of the nerve function.
Sometimes increased nociceptor drive can activate dorsal horn of spinal cord which will now respond to normal mechanosensation also [1].

Phenotypic switching is also possible [2].

PS: Both these articles are inaccessible to me at this moment. Refer them for more details.