text:
Common mistakes when sequencing?
I've sequenced two genes of 15 dogs for SNP analysis. the chromatograms of one gene looked perfect but the ones of the second gene didn't look as good. To be precise, the chromatograms of one exon looked relatively good with only a few spots where the bases seemed unreadable. But the chromatograms of the second exon were full of that. So there must have been an error somewhere and my question is where this could have happened.
My hypothesis is that I simply made a mistake during the mixing of the chemicals at some point.
Further useful information: The error must have happened befor the first pcr since i checked the pcr product with a fragment analyzer and the bands were only barely or not visible. Additionally, I noticed that many imprecisions seen in the chromatograms were only found at either the forward or backward strand.
Here is an image of several of the chromatograms of the exon that didn't work:

Looks like a dye blob.  A better job of clean up might help.
https://www.nucleics.com/DNA_sequencing_support/DNA-sequencing-dye-blobs.html

You almost give the answer yourself: the PCR doesn't look good. This might lead to insufficient PCR product to base your sequencing on. If you might have done something wrong: repeat. Otherwise try a few different conditions to get a decent amount of DNA.
Certain pieces of DNA will just sequence better than others for the same reasons PCRs sometimes work better or worse, that's why the reverse sequences might look better.
I don't know what caused the strange effect in the middle of your chromatogram. It might be a starting artifact, but also the rest of the chromatogram looks quite bad indeed.

Since i only had very limited time, I couldn't retry. I was just interested in whether one could pinpoint the problem exactly but it doesn't seem so.

Just for fun you could look at the absolute signal strength (or the scale) of your sequencing results. Probably your sequencing results are a lot closer to the noise than for a correct sequencing run.


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miRNA analysis just using BLAST against mirbase.org
I have sequencing data (Illumina). Library prep was focused on short ncRNAs. I would like to identify human miRNAs. Do you think it is feasible to simply BLAST against a current version of mirBase and filter the output for mature, human miRNAs without using bowtie/tophat against hg19 first?
Thanks

You don't need to use TopHat but it is better to use bowtie instead of BLAST. First of all you need to get rid of the adapter sequences (along with other processing steps prior to alignment).
Now there are two aspects here:

miRNA quantification
miRNA discovery

First one is relatively straightforward whereas the second one requires you to perform additional tests such as prediction of stem loops etc. There are published software that can handle both the aspects (mirDeep, miRScan etc). See this review for details on different miRNA gene finders. I have used miRdeep and it uses bowtie-1 to align.
BLAST would work but you have to set parameters which are suitable for small sequences (increase E-value cutoff, reduce word size etc). Moreover, BLAST does not have a cutoff option for the number of mismatches and the length of alignment (it only has a post alignment filter for percentage identity).
I also personally prefer bowtie because it has something called as n- alignment mode. In this mode the entire read is divided into seed and non-seed regions. You can specify the length of the seed region and the mismatch cutoff. Since for miRNAs the seed region (bases 2-8) is critical for its function, I generally set the seed mismatch cutoff to zero while allowing one or two mismatches in the non-seed region (note that in bowtie the seed always starts at 1).
In general, I would advise that you should go for miRdeep instead of BLAST. However, miRdeep doesn't straight away perform an alignment against the mature sequences. It maps the location of mature sequences in the pre-miRNA sequences (stem loops) and then aligns the reads to the pre-miRNA sequences. If the location of reads has a significant overlap with the mature region (you can adjust the window) then the read is considered as a valid miRNA.

Thanks alot. I would give bowtie a try first. So i set -N to 0. What value do you recommenf for -L (length of the seed substrings to align during multiseed alignment)?

@twckr you can set it to 10; I use 10. I set -e to 80. However, this is for the fasta file of the reads. The e option is for the max quality cutoff for mismatches. For fasta files the default quality is 40; so 80 means 2 mismatches. This would not be true if you use fastq files

I think a few mismatches in the miRNA seed might be tolerated regarding miRNA function, depending on their position.

@bli Seed is quite important. miRNAs are classified into families based on seed sequences. So, if your seed is different, it technically becomes a different miRNA. However, depending on the conditions and context seed mismatches (not exceeding two) may be tolerated.

Using bowtie I get quite different results compared to BLAST. Even setting the -L option to 22 (which should avoid any mismatches as far as I understood) I find significant differences in the results of both programs. Do you have an explanation for this finding?

@twckr You need to show me the files otherwise I cannot give an explanation. If the files are huge then just paste a section that shows the difference.

source: Stack Exchange

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

sort: votes


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What sequences are between adjacent genes?
The human genome has a lot of non-coding regions, which include regulatory elements, repetitive DNA, and introns. Suppose there are two adjacent genes on a chromosome, and their positions on the chromosome are, say,
For the first gene: 11,785,723 to 11,803,245 bp.
For the second gene: 11,806,096 to 11,806,143 bp. These values include their regulatory elements, promoter and introns as well.
So what sequence is present between bases 11,803,245 and 11,806,096? Are they satellite sequences? Is this non-coding, non-regulatory region 11,803,245 to 11,806,096 bp heterochromatin?

possible duplicate of http://biology.stackexchange.com/q/43120/3340

It is the same question, but with an additional query - are those regions heterochromatin? Are all regions of repititive DNA, like microsatellites, heterochromatin? Or is heterochromatin only the repetitive sequences of telomeres and centomeres?

No. The intergenic regions are not necessarily heterochromatin. Chromatin conformations are usually very long range and are not usually confined to a single gene. The spread of chromatin state can be prevented by insulators/boundary elements, which again are not a part of the transcribed region. The intergenic regions can also harbour distal regulatory elements such as enhancers and silencers; they can have microsatellites, transposons etc too. To know what all are there in a specific region, you can look at the different tracks in the UCSC genome browser.
In short, there can be functional and/or non-functional DNA in-between the transcribed regions.
Repeat regions need not be heterochromatinized and conversely not all heterochromatic regions consist of repeats.

Can it at least be said all repeat sequences are non-functional?

@Charles No you can't really say that. Telomeric repeats are important. So are centromeric repeats. There are non-tandem repeats like LINEs; they have been implicated in somatic heterogeneity in the brain.

Are all non-functional parts of the genome - such as non-functional satellite sequences - heterochromatinized?

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


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How can a coldblooded animal make an egg hatch?
I have chickens at home, and yesterday while removing the eggs I felt that they were quite warm. This seems to make sense, because the chicken has been brooding on it in order to make it hatch.
However now I wonder: next to chickens and/or other birds, there are other animals who are coldblooded and who are having eggs. Brooding on an egg means that the animal is delivering body temperature to the egg in order for the egg to grow and eventually produce a young animal. Now how can a coldblooded animal deliver body temperature if by definition, such an animal does not have body temperature?

Welcome to Biology.SE. The term cold-blooded is very misleading, you should have a look at this answer.

So-called "cold-blooded" animals say crocodiles and turtles lay eggs inside den or sand or mud etc. and normally not stay upon the eggs. Fishes and amphibians lay egg in water or certain specific substrate on water.  An interesting fact, commonly in case of reptiles the temperature plays a key role sex-determination.


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What causes this acorn disease?
This year, many acorns in our area (Germany, Schartzwald) fell prematurely, plagued by some kind of warts or gall-nuts which I see for the first time:

Some of the acorns are covered by two or three warts at a time, so that the actual nut itself is practically non-existent.
Judging by the hole present in all the warts, I'm guessing those were houses for some insects or larvae. Unfortunately, warts on acorns available for inspection (those which already fell) are already abandoned by their hosts.
Does anyone know who those guys are and how they look like?

tiny vespids that lay an egg in the acorn, produce an enzymatic reaction by specific chemical release that mutates the acorn into a certain shape, depending on the species, it can be that shape, or a round ball of wood, and many other galls depending on species. if you cut it open you will see a small grub or it's silk cocoon, and a little tunnel where it lived and escaped from.

The structure on the oak nut is a knopper gall.

It is a distortion of growing acorns on pedunculate oak (Quercus robur L.) trees, caused by gall wasps(Andricus quercuscalicis), which lay eggs in buds with their ovipositor.

An Andricus quercuscalicis larva in an open gall of an acorn:
Link
Here's a video by BBC on the same you may find it interesting.


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What is the origin of the name "λ phage"?
The lambda bacteriophage which infects E. coli was first discovered by Esther Lederberg  in 1950.
However, in the earliest paper on the lambda phage that I could find, I was unable to find the reason behind why the phage was named after the Greek letter λ.
Is there a source (by Lederberg or previous scientists) that mentions the etymology of this phage?

The original paper from Lederberg from January 1953 (see reference 1) indeed doesn't mention the origin of the name, but the paper in reference 2 does. It says:

The isolation of λ was first reported in 1951 by Esther Lederberg
  (119), then a Ph.D. student at the University of Wisconsin, and later
  was described, in greater detail, in a 1953 Genetics paper by Esther
  and Joshua Lederberg (120). The discovery was accidental, when a
  λ-sensitive strain of Escherichia coli K-12 (W518, obtained after UV
  irradiation) was crossed with its parent. The mixture yielded plaques,
  and the source of the virus was the K-12 parent. W518 cells that
  survived infection became stable lysogens which, like the K-12 parent,
  were immune to superinfection and which released unaltered phage.
  Although the Lederbergs were initially opposed to the notion, crosses
  between lysogens and sensitive cells led them to suggest that λ
  prophage was chromosomal and linked to gal. Joshua Lederberg recalls
  that he was convinced, from earlier work of Burnet and Lush (21), that
  lysogeny was a real phenomenon but that he “fully expected lambda to
  be a [plasmid]—in fact the term lambda was modeled after Sonneborn's
  kappa [in Paramecium; see reference 156 for a recent review], so it
  was quite a shock to discover the contrary.” (In fact, years later
  Hideo Ikeda and Jun-ichi Tomizawa [98] showed that prophage P1, unlike
  λ, is a plasmid and not part of the host chromosome!)

The mentioned kappa particle in Paramecium is an inheritable cytoplasmatic symbiont and the Lederbergs thought of something similar for their discovery. My assumption here is that lambda was the next greek letter, hence the name. The publication in which Sonneborn describes Kappa can be found in reference 3, a short historical overview on the discovery of Kappa in the review in reference 4.
References:

Genetic Studies of Lysogenicity in Escherichia Coli.
Little lambda, who made thee?
Mating Types in Paramecium Aurelia: Diverse Conditions for Mating in
Different Stocks; Occurrence, Number and Interrelations of the Types
R-body-producing bacteria.

Thanks for the well-researched answer! However, I didn't manage to find anywhere in the second paper mentioning that the phage was named lambda because it was the next letter after kappa.

@MarchHo There is indeed no direct source for that - this is my assumption. But I think it is logical, that's why I wrote it. I will edit the question and make that clearer.

@MattDMo This answer did not answer my original question, and therefore I will wait for further answers.

@MarchHo Obviously greek letters where quite commonly used for cytoplasmatic factors, see this review - the relevant piece is on page 114, right column in the upper part of the page.

My assumption is that a Lederberg discovered the Lysogen, and lambda in the Greek alphabet translates as the letter 'L' so it could be a Greek 'L' for Lederberg, or a Greek 'L' for Lysogen, or better yet a Greek 'L' for both. All of the people who were involved are deceased, so if they didn't write it down . . . . Look at all the various explanations for the origin of the name of the amber stop codons. It happened so long ago that the people who selected it don't even remember the circumstances.  Now the origin of the name of the lambda cohesive end sites as cos, that we know.


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Gene expression for mathematicians: where to start?
I am a PhD student in mathematics, and I will be involved on a project that aims to cluster (i.e. automatically group) people according to their gene expressions.
Well, the project looks very nice, but I have no idea of what gene expressions are and consequently how to model them mathematically. So here are my questions.
Is there a "Gene expression for dummies" manual that I can read, considering that my last studies of biology move back to the high school (10+ years ago)? Any suggestion, also divulgative books?
Is there a good reference to study how gene expressions are modeled under the mathematical point of view?

I suppose you first need to learn the basics of genetics before investigating the stats behind gene expression clustering. I will based my recommendations on Khan Academy, that is generally speaking a good very introductory source of information for biology and other fields.
Basics of genetics
Here are a few questions for you:

What exactly do we call the genetic code?
Are you aware that genes are transcribed into mRNA that are translated into proteins?
What is an allele?
Do you know what is an exon and an intron?
Do you know what is a TATA box?

If you answered no to any of these question I would recommend that you have a look at Khan Academy > Central Dogma.
Gene regulation
Then, you should have a look at Khan Academy > Gene regulation
Other
Don't hesitate to have a look at other sections in the biology series of khan academy if you want to broaden your understanding of e.g. what DNA looks like, what is happening at reproduction, how do genes segregate, or other things such as evolution. Typically, Khan Academy > biotechnology could also be helpful as to give you a rough feeling of the methods used to investigate gene expression
Gene expression clustering
The literature on clustering gene expression is very rich (see google scholar).

You start with the central dogma. This is the idea that information flows from DNA replication to DNA transcription and ends up in DNA translation. These are the three parts of the central dogma. The dogma suggests that DNA is the alpha and translation is the omega. There are many things in-between such as gene splicing and post-transcriptional modification. Also look at the different RNAs (small and large), because genes only lead to protein synthesis, but there are other RNA products that arise from transcription. Anorganic ions also help to synthesize proteins. They come from outside the cell and are not encoded for in DNA. That is epigenetics.
Gene clusters are genes that work together towards a common cause. That cause might be the synthesis of a protein that has a function that serves the cell. Biochemically there are many factors that contribute to a protein's synthesis and genes are some of them.
I think a math person might be interested to know that there are software packages that look for gene clusters. Here's a video:
https://www.youtube.com/watch?v=a3uiIp4gUso
There is no genes for dummies. You can build your house out of straw, wood, or stone. Here's the stone:
https://www.amazon.com/Genomes-3-T-Brown/dp/0815341385

As a mathematician who moved into biology I very much agree with your suggestion of genomes 3. Perhaps I got lucky but I managed to get one of eBay much cheaper than amazon.

I have a copy of this book,The Mathematics of Genome Analysis, it might be right up your alley (even if it is slightly dated).


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Correct term for initially neutral mutations that subsequently cannot be reversed
Can anyone tell me what the correct name is for a neutral mutation to a protein that occurs when that mutation becomes "locked in" due to a subsequent mutation?
For example: mutation A is neutral initially and can be reversed with no deleterious effects, but after mutation B, the reversal of mutation A would now become deleterious. What is the correct terminology for a mutation of A's type?

silent mutation?

Silent mutations are mutations in DNA that do not significantly alter the phenotype of the organism in which they occur. Silent mutations can occur in non-coding regions (outside of genes or within introns), or they may occur within exons.

Well, what will happen is proceeding to fixation if A does, but I don't think that really answers your question. The answer could be here.

Mutation A is a suppressor of Mutation B. The Wikipedia article on the topic (https://en.wikipedia.org/wiki/Suppressor_mutation) mostly describes situations where Mutation A occurs after B and reverses B's deleterious effects, but the principle is the same.


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Variation of length of circadian rhythm in humans in absense of time reference
Are there any studies which show the range of the length of circadian rhythms for people that are removed from actual time, (Eg no sunset/ sunrise, no clocks or other reference of time)?
For example, what proportion of people tend to have a natural 30 hour rhythm or greater?
I ask because I would like to know if it is a possible cause of insomnia, how likely insomnia is caused by this, and if this knowledge might in some way lead to solutions for insomnia

This might be the study to which you refer in your answer, the people tested averaged a daily cycle of 24 hours and 11 minutes with a surprisingly small variation in their rhythms:

The variation between our subjects, with a 95 percent level of confidence, was no more than plus or minus 16 minutes, a remarkably small range.

Worth noting they were all healthy and so it doesn't tell us much about insomnia.
This study about insomnia in adults with ADHD shows that circadian rhythms of insomnia sufferers aren't so much longer as delayed (for sleep-onset insomnia anyway). Figure 2 might be of interest, showing that insomnia sufferers have significantly delayed melatonin production.

Apparently, in one(?) study, it was shown that the natural period for humans is actually a bit greater than 24 hours.
I only know this by what Jessa Gamble said in her TED talk:
http://www.ted.com/talks/jessa_gamble_how_to_sleep?
She goes into a lot more detail, and apparently we wouldn't just have one continuous sleep each day, so that makes answering the part of the question relating to length of sleep more complicated.
But interestingly, she gets to the core of how sense of reference disturbs sleep. To quote:

The people in these studies report feeling so awake during the daytime that they realise they're experiencing true wakefulness for the first time in their lives.

Unfortunately it is sparse of detail, short, and lacks any references!


text:
What is this white-winged insect from Hong Kong?
When we were travelling in Hong Kong, near a bushy temple, we spotted some white-wing insects which we had never seen before. I sense it's a type of moth, but I have no idea what classification it is.

Tiny to 3-5mm
Mostly white on its body
Moving slowly
High volume in one area
Not so sensitive to external threats, e.g. no escaping when you try to hit them.

I think these are planthopper nymphs. I can't be sure of the species, but Ricania speculum looks rather similar:

(image source)


text:
Difference between curated publications and additional publications in nextProt database?
With reference to reference papers listed in nextProt database, what is the difference between curated publications and additional publications? Anyone using nextProt, kindly explain the terms. For example, when I search for SLC22A23 in nextProt simple search engine, I get as mentioned below on the left side toolbar.
References
Curated publications (21)
Additional publications (2)
Patents (0)
Submissions (0)
Web resources (0)
Link: https://search.nextprot.org/entry/NX_A1A5C7/
Thanks


text:
Is there any functional difference between Occipital lobe ( in mammals) and Optic lobe (vertebrates other than mammals)?
Visual processing centre in mammals and lower-vertebrates, are known to be different.
In mammals, such as human, it is the Occipital Lobe of 2 hemispheres of cerebral cortex; which is a part of forebrain. But in more lower groups of vertebrates, it is the Optic lobe, which is a part of midbrain.
(https://en.wikipedia.org/wiki/Optic_lobe, https://en.wikipedia.org/wiki/Midbrain#Corpora_quadrigemina)

Image: Placement of optic lobe, Source: http://understanding-vertebrates.weebly.com/nervous-system.html, URL: http://understanding-vertebrates.weebly.com/uploads/3/8/6/8/38682649/8113431_orig.jpg
Now, does this difference cause a difference in how the visual information is processed in their mind? such as which-features of the image extracted, how they are recalled, how they are correlated , joined  etc?

"Lower vertebrates" is a non-real, anthropocentric concept.

@kmm I meant non-mammals, and not from anthropocentric view; from evolutionary viewpoint also, "primitive", "advanced" etc are widely used in biology. If you have better terms, you could inform/ edit.

If a certain species is more "advanced" than some-other species; it doesnot  indicate the first species is more like human being. Rather, an "advanced" may be "inferior" than primitive, due to retrogressive (regressive) evolution. Primitive/Advanced is a phylogenetic concept. Those conserved some older-characteristics with changing time,  are more primitive, those replace old characteristics with new one, with change of time, are advanced.

@kmm If a plant A is more advanced than plant B; would you tell plant A is more like human being? no. Plant A or B neither are comparable this way because they were evolved in separate route than animals. Rather you could think the more-primitive plant B as quite more similar to human, because it is quite more close to common ancestor.

@kmm I did not mean a fish is inferior than human, but I meant a fish is evolutionarily primitive (/lower /earlier) than human. And that is ground reality. Terminologies made by us, agree, but the "actual thing"  is real. Wood, Oxygen, Number, Set, 1, 2 , 3, plus, minus, whatever the names are, these scientific terminologies indicate to somethic real.

@kmm Any suggestion is welcome.


text:
Why do fungi and bacteria have macroscopically distinct patterns of colonies?
Why do microbes, when incubated on an agar plate forms a distinct kind of appearance i.e., d shape of colony.
 Its kind of less unique in case of bacteria.
Bacterial colony
http://image.shutterstock.com/z/stock-photo-colonies-of-bacteria-from-sea-water-on-a-petri-dish-agar-plate-isolated-on-black-background-300465722.jpg
Fungal colony
http://textbookofbacteriology.net/penicillium_colonies.jpg
. But if we  consider fungi, an amazing kind of pattern is seen as compared to bacteria.
So, on a broad spectrum if we speak, what is the real or basic motive behind forming these specific shapes.
Does it serve any purpose in protection or any such particular reason why do they do so?
Even plant leaves do the same. I mean to say every leaf is different from eachother making itself unique..
Why is this particular pattern seen in d universe and what it has to do with the colony of microbes.

can you give some examples of what you're talking about in the question... for example... "an amazing kind of pattern is seen compared to bacteria" - what exactly do you mean? Can you attach a photo, etc?

So sorry, its pattern*.

Fungi have more variable range of colonies as compared to bacteria..tats all i wanted to say in tat particular sentence

If i directly come to the point, i would ask, why do these microbes possess different kind of colony shapes. What is the primary purpose?

Plz check the post again i've attached links with respect to the question

Well the more simplified form of this question would be this:- If we incubate different types of organism on specific medium we see different colonies or patterns for ex- fungi appears different from bacterial colonies in terms of patterns.
Even plants leaves have different symmetrical shapes. So my question is why do different living organism acquire different shape. Do these shape helps in protection  or any other  reason.

@Ashwin.N  It is about bacteria those are mostly "unicellular".  Whereas fungi, plants and animals are commonly of multicellular clusters.  So, when unicellular free-living bacterial colony on culture  medium forms a specific pattern in colony-development, it is surprising in a different way than multicellulars.


text:
Is there evidence to suggest that sleeping requires more energy than watching TV?
I have heard the claim:

sleeping requires more energy than watching TV.

I have heard the counter-claim - watching TV requires large amounts of energy.
My question is: Is there evidence to suggest that sleeping requires more energy than watching TV?

This sounds like a better fit for skeptics.SE.

It fits with biology, too.

So your sources are 3 "news" websites that don't share sources and a parenting SE post?

It sounds like you have a better one. Please enlighten us.

So you have this question after reading a couple of "news" and lifestyle sites and a parenting site, which btw do not point to any external source? I think that before worrying about who would win between an elf and a troll I should check if those thing exist. I'm not sure they do, but the links you provided aren't it.

No, I'm saying this exists in the Zeitgeist. In common conversation. It is something that people talk about. These were the sites that came up when I searched for a truth that is commonly known.

I never wrote anything about calories in my answer over at Parenting SE. I simply started that the brain is active while the body may be relaxed when kids are sitting in front of a TV. I don’t think that it’s a suitable example for your question.

From Harvard Health Publishing. The weights are in pounds, and the energy is shown in calories. These values are for over a 30 minute period.

This suggests that the claim is false; watching TV uses more energy than sleeping does.

Data is in pounds? Really? Pounds of what? Pounds sterling?

Pounds are a valid measurement of mass, see https://en.wikipedia.org/wiki/Pound_(mass). If you want me too, I can use kilograms, however for simplicity the data was in pounds and the conversion to kilograms gives decimal places, the removal of which reduces accuracy.

But that, I imagine, refers to the figures in bold. One could ask "mass of what?"  But as the question is about energy, I assume the non-bold figures are energy, which does not have units of mass.

Oh, sorry. I didn't realise that. Fixing that up now, and I'll fix the table up when I get on a PC


text:
Why would a snake follow a kayak?
We live on the shore of Kentucky Lake in Middle Tennessee and kayak often.  A common snake here is the Northern watersnake.  Observing several of these snakes over a period of ten years, I am puzzled by their behaviour in several respects.
The snakes appear in March when it's still cold, much earlier than other snakes.  They repeatedly return to the dock or the pontoon boat even after being forcibly removed. The other snakes here are shy and usually don't return once frightened away.  This year, twice, Northern watersnakes have followed my kayak.  They change course towards me and speed up to keep up.
My basic question is, Why would a snake follow a kayak?

likely they are trying to sun themselves especially in cold weather. The water is cold and they immediately try to get back on the boat.  becasue they are not as afraid of you as other snakes they are harder to discourage. They also probably can't tell the difference between your boat/dock and a log.
as for following you I can see three possible answers.
D's answer about eddies might be it.
Or they may be doing the same thing birds do with tractors, your kayak and paddles stir up the water and they are after the animals your movement scares up. A lot of small predators have learned following human machines can be a good way to find an easy meal.
Or they might hope you are a crocodile that will scare up small animals or leave scraps they can eat. Answering Hans will help understand what is happening.

I used to work with snakes, and Northern watersnakes always seemed to be the most aggressive to me, but only if disturbed.
As for them following you, the most likely reason is that your kayak was creating an eddy, supplying the snake with an easy route to follow / path of least resistance.

So the question for @Rebecca is once you stopping moving your kayak, do they still move towards you or scatter?


text:
Why do we need two markers to measure a recombination rate?
In calculating recombination,
Why is it necessary to take into account pairs of loci where one marker is heterozygous?
Why is it necessary to take into account pairs of loci where both markers are heterozygous?

If at least one locus is homozygous
If a recombination event happens between two loci where at least one is homozygous, then you would not see anything. Consider for example the following strand sequences in a diploid individual
-----A-----B----
-----a-----B----

Whether a recombination event occurs or not, the two possible chromosomes passed down to an offspring are
-----A-----B----
-----a-----B----

Therefore, you cannot tell whether recombination has occurred.
If both loci are heterozygous
Now consider the following individual
-----A-----B----
-----a-----b----

If no recombination event has occurred between the two loci of interest then the two possible chromosomes that will be passed down are
-----A-----B----
-----a-----b----

If on the other hand a recombination event has occurred between the two loci of interest then the two possible chromosomes that will be passed down are
-----A-----b----
-----a-----B----

Therefore, you can tell whether a recombination has occurred or not.

You will be a beloved instructor someday (if you are not already).


text:
Insect identification by example
Upstate NY USA here.
I am trying to identify the type of insect that this is:
Top-side:

Bottom-side:

Is this a cockroach? If so what type/sub-species might it be? If not, what other type of bug have I stumbled across here?

Size approximations would be helpful. It's not a cockroach by the looks of it; just a harmless beetle of some sort.

This is some species of Ground Beetle (family Carabidae); the trochanter of the hind leg (just before and somewhat overlapping the femur) and the threadlike antennae helps point to that group.  The book The beetles of northeastern North America by N. M. Downie and Ross H. Arnett (Sandhill Crane Press 1996; now out of print but in at least some libraries) may help with a species identification (fair warning: the keys are not profusely illustrated).


text:
What are different firing rates in different regions in the human brain?
Could it for example be that neurons that are concerned with high-order thought and medium-term planning fire more slowly, or is it expected that all neurons rather fire more or less at the same rate?
Here is an article on the average firing rate: http://aiimpacts.org/rate-of-neuron-firing/
Is the assumption that the measurements tend to be biased by accounting only for visually responsive cells warranted?

The article, has a classical engineering approach (might be wrong I just skimmed it), not that it's a bad thing. The general criticism of bias against sparsely coding neurons is correct, don't know how they can say its a factor of 10 or anything else though.
Average firing rate of one neuron only makes sense in relation to a different condition. For example in sensory neuroscience studies, we say a neuron likes a stimulus if the average firing rate of this neuron while the stimulus is presented is higher than in an equal period in the absence of the that stimulus. Conversely a neuron dislikes a stimulus when the average firing rate goes down.
Average firing rate across all neurons also is a weird measure as neurons have different baseline firing, different morphologies, are part of different circuits and have different functions in these circuits. It would be like saying that the average of a normal distribution is enough to describe it ignoring its variance.
Regarding the question itself a couple of things should be better defined: what is higher order thought? and medium time planning of what?
Neurons certainly do not all fire at the same rate, however rate implies a time constant and most importantly when one averages across multiple neurons one must have a criterion of selecting them which begs the question: Which neurons? How does one defines an area of the brain? Morphologically? Functionally? Genetically? Furthermore, what is its relevant time constant? These seem like basic obvious questions however they don't seem to have a clear and defined answer yet.
You seem to have a particular architecture in mind with multiple areas that have different functions, I assume you are modeling it. All models are wrong (yeah yeah I know its a cliche) which is to say that every model has a particular set of more or less valid assumptions. You just have to know what these assumptions are and what you can conclude given these assumptions. So basically there isn't really an answer to your question from the biology side we're still blind scientists in a dark room looking for the brain dead cat that is hiding the light switch.
Once I figure out the function of an arbitrarily defined brain area I'll let you know its time constant, then again it is arbitrarily defined and I cannot possibly figure out its function in all possible conditions without having assumptions of my own of how things should work...


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Variation of nutrients in food
Recently when buying food, mainly vegetables, I started looking at the nutritional values. Now for some reason the Dutch broccoli has way less protein (~2g/100g) than the German one (~8g/100g). Because of this I started paying attention to this and this seems to be the case with a lot of raw products. The amount vary wildly and I can't seem to find an answer to why this is. I can imagine it varying a little between yields but this seems like an awful lot.
TL;DR
How can nutritional values vary for the same raw product?
-- EDIT - 2016-09-15 --
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║               name                ║    brand     ║     PoS      ║ Country ║ frozen ║ biological ║ energy ║ energie ║ protein ║ Carbohydrate ║ - sugar ║ fat ║ Monounsaturated ║ Polyunsaturated ║ Saturated ║ Dietary fiber ║ salt  ║ price per kg ║ amount ║
║                                   ║              ║              ║         ║        ║            ║ kcal   ║ kj      ║ g       ║ g            ║ g       ║ g   ║                 ║                 ║ g         ║ g             ║ g     ║ euro         ║ g      ║
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║ AH Broccoliroosjes                ║ AH           ║ AH           ║ NL      ║      1 ║          0 ║ 27     ║ 115     ║ 4       ║ 0.8          ║ 0       ║ 0.3 ║ 0               ║ 0.2             ║ ?         ║ 2.5           ║ ?     ║ 2.07         ║ 450    ║
║ AH Broccoliroosjes voordeel       ║ AH           ║ AH           ║ NL      ║      1 ║          0 ║ 20     ║         ║ 2       ║ 2            ║ 2       ║ 0   ║ 0               ║ ?               ║ ?         ║ 3.5           ║ 0     ║ 1.99         ║ 1000   ║
║ AH Biologisch Broccoli            ║ AH           ║ AH           ║ NL      ║      0 ║          1 ║ 27     ║ 110     ║ 3       ║ 0.8          ║ 0.8     ║ 0.7 ║ ?               ║ ?               ║ 0.1       ║ 3             ║ 0.01  ║ 3.58         ║ 350    ║
║ Bonduelle Broccoli                ║ Bonduelle    ║ AH           ║ NL      ║      1 ║          0 ║ 26     ║ 109     ║ 2.4     ║ 2.4          ║ 1.2     ║ 0.3 ║ ?               ║ ?               ║ 0         ║ 2             ║ 0.02  ║ 5.5          ║ 300    ║
║ Bonduelle Broccoli                ║ Bonduelle    ║ Bonduelle    ║ NL      ║      1 ║          0 ║ 26     ║ 109     ║ 2       ║ 2.4          ║ 1.2     ║ 0.4 ║ ?               ║ ?               ║ 0.1       ║ 2.5           ║ 0.03  ║              ║ 300    ║
║ Bonduelle Broccoli                ║ Bonduelle    ║ Jumbo        ║ NL      ║      1 ║          0 ║ 26     ║ 109     ║ 2       ║ 2.4          ║ 1.2     ║ 0.4 ║ ?               ║ ?               ║ 0.1       ║ 2.5           ║ 0.03  ║ 5.17         ║ 300    ║
║ Jumbo Broccoli Roosjes Vriesvers  ║ Jumbo        ║ Jumbo        ║ NL      ║      1 ║          0 ║ 34     ║ 141     ║ 3.8     ║ 2.7          ║ 2.7     ║ 0.2 ║ ?               ║ ?               ║ 0.1       ║ 3             ║ 0.1   ║ 1.87         ║ 450    ║
║ Jumbo Broccoli Roosjes            ║ Jumbo        ║ Jumbo        ║ NL      ║      1 ║          0 ║ 27     ║ 114     ║ 3       ║ 2            ║ 2       ║ 0   ║ ?               ║ ?               ║ 0         ║ 3.6           ║ 0.1   ║ 1.93         ║ 750    ║
║ Jumbo Broccoliroosjes             ║ Jumbo        ║ Jumbo        ║ NL      ║      0 ║          0 ║ 27     ║ 114     ║ 2.9     ║ 0.8          ║ 0.5     ║ 0.7 ║ ?               ║ ?               ║ 0.1       ║ 3.1           ║ 0.1   ║ 6.14         ║ 350    ║
║ PLUS Broccoli                     ║ PLUS         ║ PLUS         ║ NL      ║      1 ║          0 ║ 27     ║ 113     ║ 3.9     ║ 0.8          ║ 0       ║ 0.3 ║ 0               ║ 0.2             ║ 0.1       ║ 2.7           ║ 0.012 ║ 1.99         ║ 1000   ║
║ PLUS Broccoli                     ║ PLUS         ║ PLUS         ║ NL      ║      1 ║          0 ║ 34     ║ 142     ║ 3.8     ║ 2.7          ║ 2.7     ║ 0.2 ║ 0.03            ║ 0.11            ║ 0.05      ║ 3             ║ 0.06  ║ 2.07         ║ 300    ║
║ Perfekt Broccoli                  ║ Perfekt      ║ Jan Linders  ║ NL      ║      1 ║          0 ║ 34     ║ 142     ║ 3.8     ║ 2.7          ║ 2.7     ║ 0.2 ║ 0.03            ║ 0.11            ║ 0.05      ║ 3             ║ 0.06  ║ 2.77         ║ 300    ║
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Do you have a reliable source for these numbers? Looking around on wikipedia I find numbers between 2,1 (French) and 3,5 (German, raw). Still some difference, but I think this could be caused by different measurement standards, different types of broccoli or  just some error somewhere. I don't expect such a large difference, as the protein in living things is always doing something, no protein no living broccoli.

I added a table based on the data provided by the stores themselves, I will add more later on.

The protein values seem to cluster around 3 gr in your table. The variation looks comparatively small to me and is easily explained by differences in species, natural variability and variation in chemical measurement of the amounts.

@pbond I agree, haven't had the time to check out the German supplies, since I live fairly close to Belgium as well I'm planning on looking into it there too.

Protein levels can vary between species or variety because all it takes is a single gene mutation to cause the plant to produce an entirely new enzyme or some other protein.  It could just be an extra pigment molecule responsible for the increase in protein level.
Also I would assume the amount of nitrogen available in the growing environment would affect the protein content greatly, as all proteins contain this element.  If less is available they can't make as much protein as another plant with a plethora of Nitrogen at its disposal.
Hope this helps :)

I added a table based on the data provided by the stores themselves, I will add more later on.


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Is beauty universal?
I don't know if this is off topic at all, but there are a lot of things that humans tend to consider beautiful which other animals in nature also seem attracted to. For example, bees pollinate the most vibrant flowers. Birds of Paradise appear to demonstrate a selective advantage to looking pretty. Peacocks flaunt their looks. Songbirds sing beautiful melodies. Butterflies are amazing. Some spider species have bright colors and perform cute dances. It seems like these examples demonstrate an evolutionary advantage not just for things that stick out from a crowd but also that look good to us humans.
So I guess my question is, is beauty universal? Are there aesthetic characteristics that are attractive to all these different kinds of animals, that would signal something good for others to see, and that different animals including humans would universally recognize as being nice?

There's plenty of things that have evolved that are considered ugly by humans. Cherry picking examples allows one to make virtually any argument seem reasonable. Voting to close as primarily opinion based because beauty is entirely subjective and individual so can't be reasonably discussed in an answer.

Not only on visual data; other-sorts of informations (Smell, Taste, Touch etc) could be beautiful (attractive in more general) or ugly/terrible (repulsive  in more general). And they are also vary from individual to individual. For say I can't imagine eat any rotten meat it smells so ugly, but a crow (Corvus sp.) grabs it joyfully.

Fitness
Fitness is a trait which, when high is pretty much always attractive to potential mates in all species. However, fitness is definitely not an "aestetic characteristic".
Traits that are often correlated with fitness
There are some "aestetic characteristics" that are correlated to fitness in many species, such as body weight. Such trait are therefore often correlated with what individuals find appealing.
Body weight is a standard examples. Heavier individuals often have better competitive abilities, better foraging abilities and therefore have a higher fitness. As a consequence body weight is often used a s a proxy for fitness.
Relative body characteristics
Novel traits in a population can be evidence of parasitism and therefore would tend to be considered as non-attractive. However, counter to this intuition, it has been shown typically in birds having high sexual selection, that individuals having novel traits are more attractive.
Why is there a lack of generalization?
To build the intuition I would just say that given the gigantic phenotypic diversity that exist among all species that perform some level of mate choice, it is pretty clear that you will not find a simple morphological trait that will be attractive to all species.
Mating preferences evolves. Individuals that are attracted toward individuals that will yield to a high progeny (and low sexual conflict and low transmission of parasites) have higher fitness their preferences increase in frequency in the population. As a consequence, individuals like whatever is (should rather say 'was') favoured in the population. Now, in some population individuals are selected to be small, or to be big or any other things. This is the process of natural selection applied to mating preferences.

I believe what you're referring to as "beauty" is completely subjective.  You say Birds of Paradise look pretty; I think otherwise.  I happen to find California Condors extremely attractive!  ;)
Cultural studies in humans show that what females view as sexy or attractive in one culture can be completely different from another.  The only common denominator seems to be an attraction towards symmetry in faces.  This has been shown by several studies in humans, but I don't know if it has ever been repeated in animals of different species.
Also different species of bees or other pollinators are attracted to different colors and smells in flowers.  They can be very selective.  Some species have a close relationship with and will only visit flowers of a single species, like the Yucca moth for example.  This again proves that "beauty" is subjective and that nothing is universally attractive.  Flowers that are visited by many species are not seen as more "beautiful."  They simply smell better, or have more nectar, or are easier to access.  I don't think there's any such thing as "beauty" in nature.  It's just an artificial label we have created...
Hope this helps!  :)

I agree with what you said. But I guess what I meant was if there is a hint of anything that inherently looks or sounds a certain way that is beautiful. I mean we can do the same thing about art, some people will say abstract art is good and others say there must be classical rules that are followed. And I for one am wholly unconvinced that abstract and classical just come down to taste, but I fear I'm veering too far into the philosophical. But maybe you can think of my question as, does nature have any "classical rules" of art that cause an above-average attraction.

Maybe I would find your answer more compelling if you demonstrated that random variation mixed with symmetry would produce the same type of ugly, normal, and beautiful distribution as what nature produces, and that then it'd be reasonable to say that we just pick out the brightly colored nice looking animals as beautiful because we coincidentally find them as nice as members of those species do (despite the near lack of colorful things in our own species). Oh, and maybe you like how vultures look more than birds of paradise, but overall people Indeed like the way the colorful birds look more.

"Is beauty universal" is a question that is haunting the scientists, philosophers, psychologists and common people for a long time. Some of them consider beauty as a subjective feeling whereas a second group of people consider it universal. Both of them have reasons to believe.
So I would try to discuss the topic in an evidence based way rather than expressing my own opinion about it.
Reasons to believe beauty is subjective -
The subjective nature of beauty in human beings is very easy to acknowledge. Here are some common examples -

Culture - Surma and Mursi women in Ethiopia wearing large lip-plate (clay or wooden plates inserted in upper or lower lip) and long necked women in Myanmar are considered to be beautiful in their respective cultures. Some cultures prefer black skin whereas most western people prefer white skin color.
Gender - a good looking man is considered more handsome to a woman that to another man. Same is true for females also.
Individual - individual perception of beauty is most diverse among all of these. What seems beautiful to me may not be so to you (I think this doesn't need further elaboration).
Specific groups - a mother finds her children beautiful even if it has some deformity.
Other species - sometimes it becomes confusing to differentiate the perception of beauty with other feelings in human and other animals. I am taking the examples you provided "Peacocks flaunt their looks." - the colorful feathers looks beautiful to most human beings. But it is actually a method to attract sexual attention of peahens (Courtship dance). Sexual attraction is a different feeling from beauty.
If the peacock example feels confusing to you, just take another easy example - most of us feel attracted to chocolates, but we may not consider it beautiful...so they are two separate feelings, right !
We love flowers, they are beautiful. But if you give a flower to a goat to admire its beauty it would at once put the flower into its mouth not even bothering to give it a glance.
Some things we feel beautiful may no have developed for that purpose at all. Tigers and zebras have those beautiful branding on their body to help them hide in grass field with two completely different purpose (one is predator and the other is a prey)
Note that awe and beauty are not the same things.

Reasons to believe that beauty is universal -
 1. In some studies symmetrical facial feature was found to be more attractive even to little children
 2. A person with good attitude and personality seems more beautiful to all.
 3. Shape of some body parts e.g. chin-shape (prominent chin in male and rounded chin in female) and vertical forehead are things that most people consider to be a part of beauty.
 4. "It is hard to find a purely biological basis of beauty", when a cat looks at you, it becomes difficult to know whether it is expecting food or is fearful or just admiring your beauty !! Much of the feeling in animals are yet to discover and thus evidences are few till now on this aspect. So, most evidences and scientific studies that you find with universal beauty are actually on human species as a whole. Studies on body shapes are an example.
 5. But if we consider attraction between animals (other than that for mating purpose) to be an indicator of the feeling of beauty, then certain properties like risk taking behavior, fitness etc may be considered to be universally beautiful.
So, there is enough evidence to consider beauty as both subjective and universal feeling.
Feel free to criticize this answer in the comment section below...but please give evidence (examples) with it, so that it can be a collection of all different thoughts in this topic. Please write down any mistake in this answer as I have written it in a hurry !!
For further knowledge you may follow these two links -
http://www.bbc.com/future/story/20150622-the-myth-of-universal-beauty
https://www.psychologytoday.com/blog/homo-consumericus/201004/beauty-culture-specific-or-universally-defined
Thank you all.

Wow I think this is a really good answer actually. I would have maybe liked a little more discussion about if it's a coincidence that what birds find attractive is what humans think is beautiful, because it seems across a huge array of bird species that where there isn't too much pressure to blend in with grasses or something, the male's way of attracting a female is by looking or sounding in a way we often consider nice or if there really is some kind of "beauty rule" applying there.


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How deep does a 0.5mm radius drill need to drill before it start to hurt the brain assuming the drill bit will be pull off without wiggle?
How deep does a 0.5mm radius drill into the brain need to drill before it start to hurt the brain permanently assuming the drill bit will be pull off without wiggle?
I am assessing how fragile of a brain is.
What are three types of damage that are most likely to happen for 3mm deep, 6mm deep or even deeper

Don't you have a drill? Just test on yourself!

@mdperry I want to do this but not after you show me how much the damage is :)

I think we need more information. Are you drilling through the bone first, because that's where the pain receptors will be. The brain itself, not so much.

@kmm It is the brain as I want to know how sophisticated a brain surgeries need to be conduct as i wanting to be a brain surgeon in the future


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Curious what this bug is
I just found this little guy crawling on me after coming in from the garden in Northern VT.  We live in a narrow grassy valley in a pretty wooded area.
This bug was crawling up my neck and when I tried to sweep him away he clung the way a tick does.  He also has a very flat profile and kind of a "hard" feeling body, but otherwise bares no resemblance to a tick.
I took this photo with my phone so it's not great.  The eyes are distinctly roundish and black. His mouth parts were visible and moving around slightly, but while I watched him he didn't appear to be trying to bite into me.
That's all I've got.

It looks like a wingless fly. I've seen something like that in an insect book.

The blurry picture makes it hard to be sure, but I'm guessing it's some sort of louse fly (family Hippoboscidae). They are typically very flat, and can lack wings. They can bite humans, but the different species are dependent on their specific hosts to reproduce.
Image of a louse fly (found on someones neck) for comparison:

(image source)

That's totally what my bug looked like.  Well done!

Found a good general-interest article about louse flies: entomologytoday.org


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Why are brightly coloured marine animals thought not to display aposematism?
There are many brightly coloured marine animals, such as fish, corals, sea stars, and octopodes. And yet Wikipaedia says it is thought that those colours don't serve to deter predators, while they do serve that purpose in insects and frogs. Why should bright colours not deter marine predators? And what, then, is their purpose?

Wikipaedia gives a few arguments, but some don't seem terribly strong, while others I don't quite understand:

It has been proposed that aposematism and mimicry is less evident in marine invertebrates than terrestrial insects because predation is a more intense selective force for many insects, which also disperse as adults rather than as larvae and have much shorter generation times.[24] Further, there is evidence that fish predators such as blueheads may adapt to visual cues more rapidly than do birds, making aposematism less effective.[30]

I read what may be four different arguments, or perhaps some together constitute one argument:

predation is a more intense selective force for many insects

Is this really true? If so, what causes this stronger pressure on insects?

insects disperse as adults

By this I presume they compare insects, whose eggs are often found clumped together in large numbers, with marine animals whose eggs are fertilised while floating around dispersed; but why does that make aposematism less useful for those marine animals? And aren't there also many marine animals whose eggs are laid in clumps on solid sea floors? Is this related to the supposedly lower pressure of predation from 1?

insects have much shorter generation times

That's very interesting: do they really have much shorter times between generations? At least a reference is made, but it is inaccessible. But how does that make aposematism more beneficial? Is this, too, related to 1?

fish predators such as blueheads may adapt to visual cues more rapidly

This, too, refers to a scientific source. The experiment showed that fish can quickly overcome instinctive aversion from certain colours (mainly red) in food. At least I understand this argument (although I'm not sure I think it provides nearly enough evidence).

Some thoughts: marine animals often do exhibit camouflage and mimicry successfully, cf. angler fish and harmful parasitic fish that mimic cleaner fish; could it be that there is something different about the metabolism of marine animals?; or could it be that the three-dimensional environment makes other strategies more effective, such as flight—but then how about all the floor-bound animals, and the unmoving ones?


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Is there an ideal evolutionary body?
I am a science fiction fan, and when I watch movies with aliens, I get annoyed at the fact that they're all humanoid. I think, "What are the chances that it will look that similar to humans?" But I wondered recently "What if there is an ideal shape for an organism in a specific environment?" An example is that all mammals have 4 limbs, and all fish have gills and fins (except for some, but I will get to that). What if that is because that is the perfect form for an organism in that kind of environment? Along with that, some fish have evolved to do certain, unique things, whether to camouflage, attack, or develop a symbiotic relationship (am I correct on that?), which brings up the question, how much does the mindset and disposition of an organism affect its end body shape, and how much more random does it make the process of evolution? What I mean to say is, say biologists were able to create organisms and watch them evolve quickly. If you took two single celled organisms that had no similarities, and put them in the exact same environment, would they evolve to look similar? Or would they develop their own, unique ways of surviving in their environment?

many fishes commit  mutually beneficial symbiotic relations. such as this-one. https://en.wikipedia.org/wiki/Cleaner_fish

This is a subject of deep interest to me since i am writing sci-fi. Trying to imagine alien life is extremely difficult if you want to make it plausible. I believe that every trait, belonging to an organism of today, had some benefit that aided survival at least once in its evolution. Then, the only reason for change would be if the trait was a detriment for survival. Thus, we have eyes that work better underwater. Rather than being the perfect creature for a certain environment today, I think that a modern lifeform would be more of a collage of traits that have been helpful over the eons.

All mammals have 4 limbs, and all fish have gills and fins (except for some, but I will get to that). What if that is because that is the perfect form for an organism in that kind of environment?

Different mammals species live in very different environments. We all have four limbs (except exceptions), not because it is adaptive to all of us for a specific environment but because there a strong phylogenetic signal. You should have a look at Why don't mammals have more than 4 limbs?.
All fishes have gills and fins (except exceptions). This is definitely because they inhabit a common environment. Gills allows fishes to get oxygen from water. Fins is a general structure that allows swimming. You will note that marine mammals also have fins (we often talk about convergent evolution) Btw, the post Do fish break a water molecule to absorb oxygen? might be of interest to you

how much does the mindset and disposition of an organism affect its end body shape, and how much more random does it make the process of evolution?

I don't really understand what you mean by "mindset" and "disposition".
Nothing is random except in the consideration of unknowns. One can make sense of a probability only by consideration of a priories. While tossing a coin is often considered as the random event by excellence, a toss of a coin is everything but random if you were to know the exact forces that apply to the coin. So asking is something is random without stating what are the a prioris you consider knowing and not knowing makes no sense (although it may make some sense in quantum physics).

say biologists were able to create organisms and watch them evolve quickly. If you took two single celled organisms that had no similarities, and put them in the exact same environment, would they evolve to look similar?

We are actually able to witness evolution in a matter of weeks in lab with organisms with short generation time such as yeast or E. coli.
The repeatability of evolution is a vast subject. The issue with such question is that it depends a lot. It depends typically on what evolution you are expecting to see and the size of the population. For example a simple change in allele frequency at a selected locus in a large population is typically very much repeatable. But if you think about larger time scale then, most think it is wise to consider that evolution would take a totally different path. There is a famous quote that says:
"If the tape of evolution were replayed a million times, a species like ours would not necessarily evolve" Stephen Jay Gould
You should have a look at Is evolution a predictive theory?.

You are in quite right-track, yes that sometimes happen, which is called "convergent evolution". It is not usually a mere coincidence, there exists a lot of advantages those led the natural selection to occur that way.
Say, fishes and mammals got separate many million years ago. Yet some sort of mammals, such as whales and dolphins got a streamline shape and quite looking like fish. It helps those mammals to swim in water. It is same for penguins, sort of birds expert in swimming in sea.
Probably you've read about homologous organs and analogous organs in school textbooks. Analogous organs (looking or working the same, but different in developmental origin, anatomy, placement etc) are usually the result of convergent evolution. (however convergent evolution could also be seen in homologous organs) Birds and insects... both contains wings. But their wings are completely different in all other aspects except look and function.
In plants also, there are events of analogy. A stem, looking like leaf (phylloclade, found in Muehlenbeckia platyclados, Epiphyllum truncatum , Phyllocactus latifrons). An inflorescence looking like flowers (members of asteraceae), tendrils of different developmental origin. (Leaf tendril of Lathyrus aphaca, Leaflet tendril of pea, Petiole tendril of Clematis sp, leaf apex tendril of Gloriosa superba, Stipular tendril of Smilax,  stem tendrix (axial bud) of Passiflora etc.) and millions of such examples are there, which are called 'metamorphosed organs'. From apparent-look they're so similar that to tell their nature is challenging. *
The most accurate similar look is found in case of mimicry, where an organism 'mimics' certain other organism due to 'cheat' certain other third party species, may it be purpose of self-protection (by hiding ownself or displaying a danger-sign) or to disguise from its prey.
1..  2..
3.

snake mimics snake : page source https://en.wikipedia.org/wiki/Mimicry .
Insect mimics leaf, page source https://simple.wikipedia.org/wiki/Leaf_insect
a plant (Arisaema speciosa) inflorescence-spathe mimiks snake's hood. image source: https://commons.wikimedia.org/wiki/File:Arisaema_speciosa_(2944482182).jpg

However, incorrect (or at-least severely disputed) statement in your question, is effect of mindset of organisms. This was told in Lamarckism, which is now almost 100% discarded, and Darwinism is proven, that tells among random inheritable variations, the favorable ones are selected.
However recent study on epigenetics showing that,some molecular tag-marks for activation/inactivation of a gene (arranged from lifestyle and environmental effects), could be inherited sometimes.

Book reference (*):

Botany, for Degree Students/ A.C. Dutta/ 6th Edition/ Oxford University Press.
College Botany/ Vol 1 by Gangulee, Das , Datta/ New Central book Agency

P.S.
However, though opinion-based, if we took 2 cells from different species (or of even same-species), evolved separately for many million years (for say in same-environment, just genetically isolated), they should give rise to 2 different kingdoms with vast difference in their structure, because evolution is a very-much chance-dependent phenomenon. Yes it is the deficit of our imagination-power to guess 'what if' there were aliens. Due to same cause, the gods and goddesses of various cultures, are highly anthropomorphic, and even having 2-types of sex. Or just like we tend-to describe non-living objects (like a kettle, conical flask or cathode-ray-tube, gear or toothbrush etc) with neck, mouth, teeth, hand, belly, etc.
There could not be any sort of "ideal" evolutionary body, just because of evolution is a chance-dependent process, where infinite thing is possible, not single, "ideal" one. I've read a sci-fi stories that tells about drugs to bring in forward(future) or backward(past) state of evolution. The first-one (future) was made a human being more intelligent. Practically if ever we could invent the first-one, we could never call it  evolution-forwarding drug because many thing is possible through evolution. It is possible to get much more stupid future-human also, through retrogressive (regressive) evolution.

Evolution doesn't plan. It's just a selection over the changes that already happened. This is important when you consider any complex adaptation.
But first, let's see a simple adaptation - the "return" of mammals to the sea, as seen with the whales. The split between the proto-whales and their land-based cousins was exactly what led to the new species - some of the population was having benefits from hunting or hiding in the sea, and it meant they were having more food than average, or their offspring survived with a higher chance or such; and among this population, being adapted to life in water was a significant evolutionary pressure. The ones that were better adapted had more food etc., so they were more likely to reproduce, and their offspring more likely to survive, and over time, they got to be bigger and bigger proportion of the whole population. Rather inevitably, they got to look quite a bit like fish - since that indeed is a shape that is exceedingly well suited to life in the sea. This is the mechanism beneath convergent evolution - two different organisms changing to be very similar due to a very similar environment.
But make no mistake - this is not a complex adaptation. All of the changes that happened during the evolution of today's whales required no pre-requisites - a change in bone length here, a more prominent diving reflex there... They didn't get gills. They didn't get an air sac. They're still mammals through-and-through.
A complex adaptation is much more rare, and quickly becomes rather fixed. First, you need an adaptation A, which must be useful on its own (remember, evolution doesn't plan ahead). Then, once the population is almost entirely made of organisms that already have A, it's possible for another beneficial adaptation, B (which depends on A), to exist and build up in the population. As time goes on, and the organisms keep changing, you might get an "updated" version of A, A', which leads to B', and a new adaptation, C, depends on A' and B'... evolution has no tool to make big changes (unless you count humans :P).
Complex adaptations are much less likely to be produced in convergent evolution (since the conditions that favoured A in the first place might not be present in another similar environment, so B will never have a chance of being useful). They also tend to be more fixed - there's a lot less place for tweaking. Consider the eye - while it has been "evolved" independently multiple times, the end results are very different. For example, our eyes have nerves in front of the sensor cells, while octopii have them the other way around. And our approach is worse, of course - it means we have the blind spot where the nerves have to go through the sensory cells, and it decreases the sensitivity of the sensory cells, since there's nerves above them. But it's extremely unlikely that this would ever be fixed naturally - the difference in the evolution happened very early, back when the complex adaptation wasn't there yet. There's no single step that could fix it now (as far as I know), and it isn't advantageous enough to have a chance of propagating in a population even if it did happen through mutation.
This is the second big point. While evolution itself isn't random (it's very statistical), mutation certainly is. Now consider any complex adaptation. You want C, because it gives you an advantage. But C needs B', which needs A', which needs B, which needs A... and each step must have been an advantage of it's own. But what if A is as advantageous as xA, but they are mutually exclusive? And if it so happens that B cannot work with xA? You'll have two populations, one of which is "stuck" on xA, while another is happily Cing. Or, as happened with us and the octopii, xA doesn't work with B, but it does work with xB, which leads to something suspiciously similar to C, yet different.
However, does this really apply to a whole alien biosphere that developed on a planet that is similar to Earth? That's quite impossible to tell. All life on Earth we know of is made of RNA, for example. This doesn't necessarily mean that RNA is the best ever - it may just mean that once RNA appeared, nothing else could survive, or there were complex adaptations that quickly got grafted on top of RNA. DNA is just an "update" on top of RNA - we use it for "main data storage", but it's usually transcribed to RNA before it gets used to build proteins, and signal, and all the other roles RNA has in the body. Every organism on Earth that we know of has a common ancestor - but that doesn't mean that the common ancestor is inevitable, or the best. It may just mean that once life existed, it consumed every other bit of proto-life it found. There's a good chance that new life from scratch simply cannot appear in an environment that's already settled by another form of life.
However, I would hazard a guess that the way aliens most often look in fiction is way too human. There's plenty of things that are 100% "accidental" in the whole ancestry of a modern human. Opposable thumbs sound useful for any tool-making creatures that use a muscle+bone combo; the fact that we have five fingers isn't. The way our heads are shaped is heavily built around the way many individual adaptations shaped our complex adaptations, and is unlikely to be similar elsewhere. A common trope in sci-fi is to have alien species which are humanoid reptiles, or humanoid avians, for example; but why would a humanoid reptile-like female have breasts? Or five fingers? Or hair? Bi-lateral symmetry is almost omni-present in mammals, and it sounds kind of right (it makes many things simpler, it yields well to manipulation and observation in a 3D environment...), but is it really something that would be universal in intelligent aliens?
That said, obviously the aliens in sci-fi (especially movies and TV shows) are designed in such a way to a) make it easier for humans to play aliens, b) make it easier for humans to relate to the aliens, both on-screen and in theatre, c) avoid making silly mistakes in the design of such aliens. Some shows try to handwave this or even outright justify it (the humanoid cats in Red Dwarf had a huge bonus from being as close to human as possible, since they were living on a ship that was designed for humans), with various levels of success (right, Star Trek, seeding life five billion years in the past is totally going to produce similar alien species five billion years later).

The language is quite complex  for a scientific answer, and in many places I'm having difficulty to find a whole meaning of few successive sentences.  You could try to write in more simple language, and could try shorten the text if some parts are not extremely-essential.

For mathematical steps you provided, could break into separate lines.

@AlwaysConfused Well, I'm not a native english speaker, so I have no idea what you consider complex here. Except for the trait dependencies, which simply are complex - that's the whole point. And I'm not sure what you mean by "mathematical steps". Apart from not providing multiple examples, I'm not sure what would make sense to remove - the question skirts a border between World Building and Biology.

I'm also non-native in English, as well I'm not a site-moderator. It was just a feedback or polite suggestion. Maybe the sentences are quite long so I'm having trouble to clearly extract the meaning. For say, the second-paragraph, "But first...the split between... convergent evolution"  it could be wrote as "for say, a group of mammals (now called as proto-whales), were got separated from the land-population, and  evolved in marine condition. later on they took a fish-like shape though they are not fish". That may quite less-artistic, but easier to understand, that I meant.

The polite suggestion is not specific for this-one answer. rather future suggestion.

By 'mathematical steps' I meant the 6th paragraph, i.e. "This is the second big point... B cannot work with xA... yet different" that paragraph.

As well I gave an upvote to this answer because I found a lots of short-sized informations new and helpful to me.


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Why are animals afraid of the vet?
I can understand why people are afraid of the doctor, because they have mental concepts of health and medicine.
But why should an animal be any more afraid of the vet than the post office or any other public space?
It doesn't seem like they would understand why they are there or what possible consequences it could have, the same way a human would being in a hospital.

They just don't like being manipulated the way they are. The same reason why you don't like to go to the dentist.

Rather opposite. If I'm ill i'n NOT affraid of the doctor because I "have the concept of" health, medicine and curing. Rather animals ARE affraid because they don't have the concept of health and medicine-action. If I had not "that"-concept, I would probably behave "inhuman" (within quotes); in the doctor's chamber

Because most dogs are not "dumb animals". Cats are more mysterious, and I've never taken one to a vet, so I won't speak to their behavior there.

Most animals are not afraid of the vet. When I was in practice, many dogs and cats waltzed in perfectly happily.
Of those that were afraid, I presume that many picked up expectations from their owner.  The owners who tell themselves "My dog is going to be afraid of the vet!" will be tense and nervous themselves, and of course their pet will detect this and react the same way. Many owners were far more distressed than their pets were, expecting some huge negative reaction to the vaccination or something (the pet often didn't even notice the injection, until the owner squealed or shrieked with anxiety).
Finally, animals that experienced something negative on a previous visit -- perhaps a bad interaction with another animal in the waiting room, or their owner being afraid of needles, or actually having some unpleasant procedure -- will of course remember this.

My dogs are not afraid of the vet either. They are a little bit cowed by all the smells and sounds in the waiting room, but once in a room with the vet, they are more relaxed and quite cooperative. An occasional yawn and the relative lack of tail wagging suggests they aren't stupid about it, though.


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Why antipyretics do not bring the body-temperature below normal?
Antipyretics like paracetamol are used to decrease the body-temperature in fever patients.
But some of them are also used as pain-killers in sprain or other injuries (where there's no fever). In that case they changes the body temperature very little (if any).
Why? Is there any molecular mechanism responsible for  this?

Acetaminophen (paracetamol) induces hypothermia during acute cold stress (2017)

Antipyretics doesn't work by reducing the body temperature but blocking pathways that make it higher.
For paracetamol/acetaminophen the mechanisms implied are not currently completely clear (as reported on Wikipedia or on Katzung's "Basic & Clinical Pharmacology").
For the most common NSAIDs (aspirin, ibuprofen, naproxen, ...) the mechanisms instead are more clear as they block some enzymes that are involved in production on inflammatory molecules (enzymes COX1 and COX2 that are implied in the arachidonic acid pathway as said on this article).
When these inflammatory molecules rise concentration in blood they can get to the hypothalamus so it will set the body temperature at an higher level; when these signals stop coming (inflammation stops or no more molecules are produced because of drug's block) the hypothalamus sets the temperature to the normal range.
More infos about hypothalamic temperature set point.

Ibuprofen acts as antipyretic?

Of course yes (but paracetamol is preferred if only anipyretic effect is needed). For example ibuprofen in Italy is the only official alternative to pracetamol as antipyretic in paediatric patients.


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Why not surgically resect the tumor before CAR-T cell therapy? Won't that be more efficient?
If CAR-T cell therapies suffer from tumor antigenic escape, why not just resect the tumor via surgery, leaving behind a small number of cancerous cells, and then wipe them out with CAR-T cells? The small number of cancerous cells may reduce the chance of too many cancerous cells escaping CAR-T cell cytotoxic killing that may cause tumor regrowth.

Can you please make yourself familiar with cancer therapy? Every cancer which can be operated is usually operated to reduce the tumor burden for the patient. And to raise the chances for other therapies to be successful.

To give an appropriate answer is needed to know which type of tumor and the grade of the tumor, because there are specific protocols redacted by medical consensus conferences for each of them.

I second what @Chris said. As it is now, your question is too undefined to provide a good answer. You're touching on interesting subjects, though. Maybe you can either refine your question to be more specific to a type of tumor, or ask for information on CAR-T therapies more generally?

You've deleted all of your previous questions about CAR T cells, which isn't advisable. However, you don't seem to understand much about cancer therapy in general, and immunotherapy specifically. I would strongly suggest finding several good review articles or reliable websites about the type(s) of cancer you're interested in to get an idea of how cancer therapy works in general (surgical resection, chemotherapy, radiation, immunotherapy, combination therapies, etc.), then move on to understanding immunotherapies in general, then you can begin to apply your recent research on CAR T cells.

please read the answer below and follow the links in it, I hope that would resolve this conflict.

CAR-T cell therapy (Chimeric Antigen Receptor-T cell Therapy) is most effective in treating hematological malignancies. Hematological malignancies (known as blood cancers in common parlance) mean the cancers produced due to over-proliferation of hematopoietic stem cells and the liberation of the immature cells into the circulation . Till now all clinical trials of CAR-T cell therapy has seen more and more success. With the development of second, third and fourth generation (also called TRUCK T cells) CAR-T cells the percentage of remission is increasing. But  almost all these advances are in hematological malignancies.
Clinical trials on solid tumors has shown that the "efficacy is not as remarkable as in the case of hematological malignancies".
The question asked was about resection of the tumor before treating with CAR-T cell therapy. This question is valid only in case of solid tumors (you can't resect blood as it is liquid). As I already said this therapy is only used for blood cancer till now, so there is no question of surgery before the therapy.
I think I could answer your query above. If you want to gain more knowledge, then read below -

The best use of this therapy in blood cancers is after hemato-poietic stem cell transplantation (note that it is not surgical resection)
If you ask, why this therapy was not successful in solid tumors, I would recommend to read the review published in Springer with the title "Hurdles of CAR-T cell-based cancer immunotherapy directed against solid tumors".

Recently however there are new developments that are helping to apply this immunotherapeutic procedure in case of solid tumors also and in that case it is usually given after surgical resection.


text:
Is every decision we make already "pre-programmed" because of DNA?
DNA has information about our cells and how every cell should act.
Since I am made entirely of cells, including things that make my mind, aren't decisions coded for by DNA by proxy of our cells.
Even asking this question is a decision that has already been made because that's what my DNA told my cells to do?

There are so many other factors, some that we know like epigenetics, upbringing, the environment, and probably others we don't know like how exactly our brain takes a decision. No, I don't think your DNA makes your decisions. But it influences them.

DNA seen to be code our structures, and structures determine the functions. Similarly, nervous system's structure (also dependent on codes of DNA) determine its function. Though DNA is not the sole factor for decision making, but it is an important factor. Otherwise different organisms (reptile, bird, human etc) would not behave differently.

Sometimes many complicated tasks or decisions depend solely upon genetic composition (at least apparently), such as weaving the web by spiders

This question appears subjective, but I think can somewhat be answered in an objective framework so long as we avoid "I reckon" answers. We should answer it here rather than flagging as a duplicate of philosophy SE because biology comes at this from a different angle.

There is a misconception of the information coded in DNA here, but to me this seems more like a fundamental question about free will versus determinism.

@arboviral I'm keen to have a question that comes at that debate from a biology PoV where we can have scientific contributions to an answer about what biological stuff contributes to our thoughts and sensation of "free will" (I think Remi.b and I have provided some reasonable answers already). If you have any suggestions on how to shift the focus away from top down arguments, to bottom up ones, please do suggest an edit to the Q!

@James fair enough. I've suggested a slight edit to the title that makes it sound more 'biological'.

Incidentally it's been twenty years since I read it so I can't write an answer based on it from memory, but from what I remember 'The Extended Phenotype' (from back when Dawkins stuck to writing interesting books) essentially takes the opposite view from the existing answers and argues that genes do determine our behaviour. You (OP) might find it an interesting read, assuming it isn't what prompted this question, although it's probably dated a bit. You might want to start with Selfish Gene though - it's essentially a sequel.

Just a detail of semantic for your title; "DNA" is not an explanation (or a hypothesis), it is a molecule. "our decision are dictated by our DNA only" is an explanation (or a hypothesis). Saying "decsions are pre-programmed because of DNA" would be like saying "Paul will be here soon because of car". It does not mean anything. "Paul will be here soon because he took his car" would be correct, as "he took his car" is an explanation (hypothesis) but "car" is not.

"Do we have free will?" It's a big question.
DNA (among other epigenetic factors) code for proteins, so ultimately it determine our cells, which in turn are responsible for our neurology, although how this translates to behavior is variable depending on factors beyond DNA@Remi.b's answer. De facto you're asking about the extent that our brain structure and neural activity determines our conscious stream. This boils down to "Do we have free will?". That question historically was only accessible to philosophers. It is now accessible (but not completely answerable) to biologists, more specifically neuroscientists. It's a great question, but is still open to a lot of subjectivity.
An evolutionary explanation.
Anil Seth, professor of cognitive and computational neuroscience at the Sackler Centre at the University of Sussex, gives a very good answer to the question at 25:44 in this BBC Life Scientific interview.

We are determined to have it in both senses of the word...
Yes, we do have free will because we can behave the way we wish to behave. We cannot decide what to will.

Paraphrasing the guts of the answer: it's very important for the brain to differentiate between internalized experience, and reflex.
Reflex, such as placing your hand on a hot stove, never reach the "conscious stream". These have an obvious correct choice; in this case, removing the hand from a hot stove is clearly the right choice, every time.
Then there is internalized experience. Complex problems have many potential losses and gains. To cope with this, the brain needs to internalize, reflect, and is taking note and making a plan; the sensation of free will. By taking note of that situation within it's context and the plan, we can perhaps change our actions the next time we encounter a similar event so that we can optimize our choices to attempt to cause the least damage to ourselves and/or maximize the benefit.
How is learning achieved.
We have established that there is a need for new memories to form in order to solve complex problems. Long term memories are the result of new physical synaptic connections in the brain. This connection endures whether it’s being used or not.
Psychologists put these into two broad types are two kinds, implicit (akin to reflex; how to read, how to play your favorite song on an instrument etc.) and explicit (the things we are consciously aware of). Explicit memory comes in two forms: episodic and semantic (Tulving, 1972). (i) Episodic memory includes experience. For example, that time you planted some seeds and a potato grew. (ii) Semantic memory is abstract to your own experience. Something more like "Primordial potatoes originated in southern Peru".

To bring this back to the original question "Is every decision we make already pre-programmed because of DNA?" It's long winded. Our choices are built upon the results of our past choices in a given environment. We are able to make these choices, to an extent depending also on other variables, because of the products and machinery encoded in our DNA.
The philosophers answer
If this answer is a bit scary or makes your choices seem futile, you can simply sit around and do nothing instead of doing whatever you normally would do; it's your choice.
See a similar question answered from a different perspective over at Philosophy.SE.

Your answer is drawn from philosophy and not from science. If this is what the OP what expecting, then the question is off-topic on Biology.SE.

I'm presenting the (brief) opinion of a scientific expert in the field. This is not philosophy, but you're right it's not science either. There is currently no empirically falsifiable hypothesis surrounding free will (even the same environment in controlled twin studies will lead to different experiences for either twin; it's not good enough). Presented in this answer are good reasons why the sensation of choice should exist despite a rigid framework of genetics and environment that determine our phenotypes. I've removed some fluffy wording, but there is still room for improvement!

Is every decision we make already pre-programmed because of DNA?

No! An obvious way to realize this is to compare identical twins. While two randomly chosen twins ressemble each other (in terms of appearance but also in terms of behaviour) more than two randomly sampled individuals in the population, it is still true that they are not exactly identical. So something else than DNA must affect behaviour. What is it?
Phenotypic trait
Let's first define what a phenotypic trait is. Broadly speaking, the phenotype is the consequence of the genotype on the world. Loosely speaking, a phenotypic trait is any trait that an individual is made of! This includes the colour of the hair, the behaviour, the nature of emotions and the decisions. Decisions are nothing but the phenotype of a person.
Phenotypic variance
For any trait, you may (or may not) see variation for this specific trait in a population. You can therefore calculate a phenotypic variance for a specific trait and then wonder what is causing this variance. Is it only DNA or is there something else in play? Let's call the phenotypic variance for a given trait $V_P$
What is causing phenotypic variance
Why would a population display any phenotypic variance? Why wouldn't we just look exactly asame? What explain these differences?
There are two main sources of variance that are underlying this phenotypic variance. The first one is the genetic variance and the second one is the environmental variance. We will call the genetic variance $V_G$ and the environment variance $V_E$.
To appreciate the role of genetic variance $V_G$, consider comparing difference in height among countries as an example. To appreciate the role of environmental variance $V_E$, consider comparing the body shape of people eating at McDonald and those that don't.
So does $V_P=V_G+V_E$?
Is there something else than environmental and genetic variance that explains the phenotypic variance? The answer is yes. Therefore $V_P>V_G+V_E$. So what is this something that causes this inequality?
Gene effects and environmental effects covariance
Well, first there is a potential non-zero covariance between the environment and the genes. Let's call it $COV(E,G)$. For example, thinking of animals that compete for territory, individuals that have alleles (an allele is the variant of a gene) that make them bigger might be better competitor and have access to bigger territory and therefore to more food which in turn will make them bigger. In such case, there is a positive covariance (or positive correlation) between gene effects and environemtnal effects.
Developmental noise
The developmental process can be quite noisy. An obvious way to appreciate its noisiness is to acknowledge differences between right and left side of people's face. Such noise bring some variance in phenotypic trait in the popualtion. let's cal the contribution of this variance $V_{DN}$. Of course, the amount of developmental noise might depends upon the environment or the genes so that we should also consider covariances.
Epigenetics
Epigenetics also yield to some variance and epigenetic effects may well covariate with gene effects, environmental effects and the effect of developmental noise, so again we should consider all covariances. Let's call the variance due to epigenetic effects $V_{I}$.
Putting all these variances together
So, if $V_P=V_G+V_E$ is inaccurate, $V_P = V_G + V_E + V_I + V_{DN} + COV(V_G, V_E) + COV(V_G, V_I) + COV(V_G, V_{DN}) + COV(V_E, V_I) + COV(V_E, V_{DN}) + COV(V_I, V_{DN})$ would be a bit more correct.
Coming back to the question
So, genes do explain part of the variance in behaviour and appearances in human (or any other living being) populations. But it is by far, not the whole thing! The things one experiences through its life typically will greatly affect its future decisions.
Source for a more complete answer
If you are looking for definitions that are a bit more rigorous than those I have been using here, or for a more complete explanation, then you should definitely have a look at my answer at the post Why is a heritability coefficient not an index of “how genetic” something is?. It will also teach you the concept of heritability.

Please leave a comment when down voting (2 down votes for the moment)!

I like this as a complete answer for "Are we more than our genes?". You clearly show that there are a lot of variations in our traits that cannot simply be explained by our genetics. However the answer is missing a step between "our genes don't determine our traits" and "our genes don't determine our choices". I'm not exactly sure what that step looks like, but I'm sure it exists!

By the way, I'm not one of the down voters (just an onlooker), and whilst hit and run down voting is annoying, there is and should not be an obligation to explain down votes. That's a discussion for somewhere else perhaps!

A behaviour is a phenotypic trait. Any choice is part of our phenotypic trait. There is no step missing.

I agree with you concerning down votes. After two down votes I ought to assume that something must be wrong in my answer but don't know what.

My only suggestion would be a section trying to define choice as a behavior, and behavior as a phenotype (which are not necessarily dependent on DNA). However, using general rules about phenotype variance independent of DNA to explain the differences in sensation of how two people take the red pill, or the blue pill isn't an entirely satisfying answer. In my answer I discuss what possible benefit the behavior of choice might have in terms of survival, which is more superficial, but satisfying!

Thanks. I extended my definition of phenotype to clarify that behaviour and choices are part of the phenotype.

As Remi already explained, there can be phenotypic variations even if the genotype is the same. This is applicable in a broad sense. I'll focus on your query on decision making.
DNA does encode the developmental programmes in the body (including the brain). Because of conserved developmental programmes, we do have some very basic instincts and reflexes that are usually common between different people (as infants and to some extent, as grown ups too).
However, while the gross developmental programme of the brain is conserved (brain organization etc), memories and other learned preferences arise because of experience. At the cellular scale, neurons establish synapses with multiple other neurons. Experiences either strengthen or weaken the synapse. These experiences are based on how often (and in what way) these neural connections are used, which is in turn based on interactions with the external world. The DNA does have the information to allow the cell to carry out the processes that can strengthen or weaken a synapse but it does not have the prior information of which synapse to strengthen (this is somewhat grossly analogous to body-building, just that you are not always consciously aware of which neural circuits you are training).
Apart from that, there are several cellular processes that are inherently stochastic in nature. The effect of stochasticity dominates when the number of the participating entities in the system is small (such as a few neurons deciding which other neuron to interact with). In such conditions, deterministic models cannot explain the outcome. The stochasticity is also the source of the gene expression noise. When we say that stochastic effects dominate, it means that the system dynamics are governed by probabilities and not fixed deterministic rates.

So the bottomline is:
Decisions are not pre-coded in the DNA, but the ability to gather information and make decisions, is.
So it all depends on what information you gather.

that would be ridiculous. though the situations that we encounter may be quite similar to those for others of the past, we must decide anew what to do in each situation. it is not written in our dna what will happen.