botany - How to decide which is the correct scientific name for a particular species

When it comes to plants and animals, common names clearly differ from region to region.

A first effort to univocally classify them was done in the 16th century by Carl Linnæus (see my answer to this question for some historical background).

The nomenclature of plants is governed by the International Code of Nomenclature for algae, fungi, and plants (ICN), and for animals from the International Code of Zoological Nomenclature (ICZN).

The fact that there are rules, however, does not imply that names are conserved over time, nor that there is a rule for everything!

As time goes by rules change, certain species may be assimilated by others, or a certain subspecies will separate and become its own, and at times name changing proposals even raise havoc in the scientific community.

In summary, it is important to remember that taxonomy poses rules that are there to facilitate talking about science. Those are not absolute rules, sometimes they are arbitrary, and therefore for certain species there is no univocal name (and surely there is no correct name).

bioinformatics - Is it possible to add a new sequence to a blast database without recreating it from scratch?

You can use blastdbcmd to extract FASTA sequences from the BLAST database. Then you can append your extra sequence to the newly created FASTA file, and remake the BLAST DB using makeblastdb. Assuming you have a protein BLAST database in the current working directory, and a sequence you want to add to it in new.fa:

$ blastdbcmd -db proteindb -dbtype prot -out db.fa -entry all
    $ cat new.fa >> db.fa
$ makeblastdb -in db.fa -out newproteindb -dbtype prot

(Replace prot with nucl if you have a nucleotide database)

Online Molecular and Cellular Biology Video Lectures?

I am looking for video lectures to go through to guide my reading in intro molecular and cellular biology. I've had intro bio and I study evolutionary theory, but my molecule- and cell-level knowledge is weak.

I'm finding it impossible to know where to look in a big book like Alberts, or to read Lodish without a guide, so I really need lectures to help me out. I've tried the MIT OCW assignments and a few other similar sites, but I can't seem to find a course that includes lectures. Does anyone know of any? Ideally they'd follow Watson et al. for molecular and Lodish for cellular, but I can find other textbooks too.

genomes - harvesting fertilized eggs from Tetraodontidae species?

I would like to know how easy/difficult it is to harvest fertilized eggs from Tetraodontidae species such as Tetraodon nigroviridis or Takifugu rubripes compared to zebrafish? Ultimately, I would like to know how much material would be obtainable from Tetraodontidae eggs to extract DNA from the nuclei.

I know zebrafish lay lots of eggs, and other model fish species like medaka lay much fewer of them, but I couldn't find any information about Tetraodon nigroviridis or Takifugu rubripes after some googling.

neuroscience - Is there a biophysical causation from local field potential (LFP) to spikes?

Many experiments showed that neurons tend to fire at some phase (usually trough) of local field potential (LFP) oscillations, such as theta or gamma rhythm. LFP is supposedly generated by a population of neurons with coherent currents induced by spikes. So there is a causal link from spiking activity to LFPs. Is there also a significant influence on the spikes directly from LFP (not via the hidden spikes that generated the LFP)?

Is it just an epiphenomenon, and or is there a possibility that it is partly a serious mechanism for neural computation?

food - What impacts on metabolism are likely from the 6x increase in water consumption by Americans at restaurants since the 1950s?

As mentioned by nico in his comment, this infographic is very misleading in that it presents quite uninteresting data in a way as if it was a sensation.

It claims the average meal drink has been soda which has increased by 6 times in size. Then it claims most of the volume is water. This is of course true. But while a substance solved in water barely increases its volume, it can still make a difference - soda and water are completely different things and the important statistic to look at here is not the amount of water drunk, but rather the fact that it is soda. Where I live, soda usually contains around 27g of sugar per 240ml (8oz) which is 9% of the GDA. So according to this data, people consume half their energy needs of that day with the drink they get in their restaurant meal.

The other statistic is about calories per ounce of the food. What sense does a statistic about that make? The only relevance of the calorie density of food would be the effect on how well it is digested, and for that only a calorie number isn't really helpful. The relative ratios of fibre, carbohydrates and fats would be much more useful in that case. The only interesting statistic here is that meals have almost doubled in size. The fact that the volume of meals has increased much more hints that there is a higher portion of less calorific foods, such as salads.

Impact on metabolism? Hard to say, this is a statistic about what people eat at restaurants, which is not really something that you expect to reflect their refular diet. It doesn't tell you anything about their general lifestyle, which would be the relevant statistic for effects on metabolism. If you only look at restaurant meals, those could look really unhealthy but on the larger scale, people balance it out in their every day diet and general lifestyle. If you had an additional statistic that shows that people actually eat a significiant amount of meals at restaurants, and they're the kind of meals described by the infographic you gave, that would have some implications.

neuroscience - Somatosensory System - Biology

I have a test in my upcoming Neuroscience class, one of the items on the study guide is:

Identify 2 means by which a maintained, constant stimulus produces only a transient excitation of the Pacinian corpuscle (phasic receptor). How does adaptation occur?