#i know you want to just discuss the passing on of encoded traits.

[inmirova]

I hate having to take lower-level classes not necessarily because they're boring but because I feel the need to fill in additional information in my answers and notes so it takes me twice as long. why was jean-baptiste lamarck wrong in his theory of inheritance of acquired characteristics? well the problem is he was almost right but we're not learning that right now.

[fellmother-archive]

{The Inheritance of Holy Blood}

{ ooc. I think I should preface this by saying that I am currently studying a bachelor’s degree in molecular genetics and biotechnology which is why this meta is so long, so if there is anything in this that you do not understand/want to know about, feel free to message me! If you wish to dispute something, please come to me with factual/canon reasons why the concepts I’ve put forward are incorrect-- not ‘this conflicts with my hc so it’s wrong and I don’t need to explain why’. Anyway, I’ve tried my best to explain certain concepts and how they work in this, so let’s get this thing rolling- }

     To start this off, it would be easier to address one misconception that seems to be rampant within the community when discussing how holy blood is inherited:

     The inheritance of holy blood is not sex-linked, as none of the family trees display a pattern indicative of it being linked to either the x or y chromosome, and the presence of methylation in imprinting does not work for this either. If this was the case, Arvis and Saias could not have major Fjalar, and Sigurd could not have major Baldr. Assuming this would also mean ignoring what has been said about holy blood inheritance in fe4’s playing guide— ‘it doesn’t matter if the person is the eldest child or if they’re male, there is no rule’.

     Instead, holy blood is inherited through a much more complicated means, regulated by various factors that, in theory, give the results that can be seen in throughout the Jugdral family trees, but also do not have a strict set of rules for them. When looking at the pedigrees, and if someone with minor blood is a carrier, you get results such as these:

Fjalar:

Naga:

Loptyr:

Thrud:

     Looking at the pedigrees in such a manner, however, is incorrect—there is no distinct pattern that can be discerned, nor are there enough generations to firmly put forward a simple method of inheritance. Though it looks to be a recessive gene, there are glaring exceptions which show that it simply cannot be inherited through that way—in the case of the pedigrees shown above, Deirdre and Julia’s case of having major Naga, Saias having major Fjalar, Arvis having major Fjalar, and Ishtar having major Thrud.

     There are also instances where a parent with major holy blood does not pass anything onto their offspring which also means that looking at holy blood in this way is incorrect—how Lewyn’s father possessed major holy blood, however his brothers had nothing.

     Due to this, holy blood cannot be assumed as someone having minor blood only inheriting one recessive gene, or major blood being someone who has inherited two recessive genes. Instead, the listings of what holy blood an individual has, and whether it is major or minor, should be interpreted as the character’s phenotype—what they express—rather than their genotype. Looking at it this way, a proper inheritance pattern can be seen, and it becomes exceedingly clear that all types of holy blood are more likely to be a dominant gene with decreased penetrance, and variable expressivity. So that it makes more sense, each factor will be explained.

     The reason as to why holy blood would be dominant gene is simply because in almost all cases, the blood is passed on in some way or another and is presented in their phenotype. It is the level of expressivity of the blood in the offspring that changes. If it was a recessive gene, then a carrier would not show any sort of expression related to the blood they have inherited, however that is not the case, as in fe4, minor holders of holy blood still express their lineage through the bonuses that are added onto their growths. This leads onto another factor regulating the gene—variable expressivity.

     Variable expressivity is when people with the same genotype display a range of different phenotypes, however the trait will still be expressed. An example of those would be if you had a group of the same species of organism that all have identical genotypes, with a specific gene encoding for dark brown fur, however all the individuals in the group expressed a range of different shades of brown without another gene that contributes to fur colour or inhibited the expression of said trait. Below is a visual representation of this example, with each square having the genotype Bb—where ‘B’ is the dominant allele that encodes for dark brown, and ‘b’ is a recessive allele that has no impact on colour.

     This concept can be applied to holy blood, with major blood being when the trait is fully expressed, and minor being when it is not. This explains why in certain family trees, such as the Fjalar, Thrud, Forseti, and Baldr ones, the offspring manifest minor holy blood, despite one of their parents having the corresponding major holy blood—they inherited the gene, it just is not being fully expressed. Does this mean that an offspring could potentially have two major holy blood groups? Technically yes, however if this is incompatible with life, then one of the holy blood’s expression would be inhibited slightly, resulting in minor blood.     This also explains how Lissa from fe13 can be born from at least one parent who presumably had major Naga, and not possess a brand, but how Owain can have major Naga. By extension, this also explains how the Grimleal’s breeding program could have spanned over a thousand years without a vessel/someone with major fell blood being born, despite starting with someone who has major fell blood.

     NOTE: decreased expressivity does not mean that the trait/blood has ‘diluted’. They have the same genotype as someone with major blood—it is just being expressed at a lesser level. You cannot ‘dilute’ a gene.

     Decreased penetrance is quite similar to expressivity, however it is a different regulating factor in its entirety. While expressivity deals with individuals having the same genotype, but displaying a certain trait to varying levels, decreased penetrance is when a dominant trait is inherited, but the trait does not manifest. If a dominant allele can be inherited, but not all the individuals with that genotype develop the trait, then it fits under this category. Using the same example as before, this would be if you had another group of those organisms with the same genotype, but some of them did not express dark brown fur at all.

     Despite the lack of expressing the trait, however, they can still pass it down to their offspring—they still have the allele that codes for that specific trait. This explains why an offspring will not express any sort of holy blood, despite their parents having either major or minor blood for that type—why some offspring, such as Daccar and Maios, do not have major or minor holy blood, despite their father possessing the former. It can also explain, specifically for fe15, why Alm and Celica have major blood, but why none of the ancestors before them did.

     When you mix these two factors together, using the same example as before, you would get a genotype that can express itself like this in a population:

     If we were to translate this into holy blood, it starts to match up to the trends seen in the family trees—the dark blue being major blood, the white being nothing expressed, and every shade between those two being minor blood. Every square has the genotype N?, with ‘N’ being the dominant allele encoding for major Naga blood, and ‘?’ being an allele that does not impact on the expressivity of the other.

     So then, what about the situation with Julius? If an offspring inherits one allele for a certain type of holy blood from each parent, what was the point of having two people with minor Loptyr produce an offspring? In this case, it was not necessarily the fact that he has two parents with minor Loptyr that resulted in him having major Loptyr, it is instead that he inherited the allele from Deidre, with his Fjalar blood obviously coming from his father and it was expressed fully. The chances of this happening were increased drastically by having two parents with the allele for Loptyr blood, as he could have inherited one from Deirdre, one from Arvis or both instead of just Deirdre or Arvis.

F= Fjalar, N= Naga, L= Loptyr, ?= unknown allele (not coding for Loptyr blood)

     As you can see, the potential offspring go from 50% of them inheriting the Loptyr blood allele to 75%, which is a considerable amount, and enough to almost ensure that the child will inherit at least one allele for that holy blood.

     Does this still work in Saias’ case if it turns out that canon decides to confirm that he inherited minor Loptyr from his father? Yes, actually—it would be a result of error or mutation during meiosis on Arvis’ side of things—whether it be from nondisjunction, an addition or translocation on the chromosome containing the genes, or from something as simple as the section containing the gene encoding for Loptyr blood crossing over to the chromosome that already has the gene encoding for Fjalar blood.

[thelonelyandroid]

Someone talk to meeeee!

Tbh I want to tackle the question of whether or not Data is a "philosophical zombie" if anyone wants to bite... Like... Does he really pass the Turing test? I guess so, given that typically his answers to questions seem like a really pedantic guy just talking to you. Ask him if he likes cats, he says yes. Ask him if he likes The Borg, he says no. Ask him his hobbies, he'll remark upon Sherlock LARPing and painting as his main hobbies, among other activities. He's expressed that he wishes for companionship, even a family with children who he wishes to have had a hand in their creation. He can become irritated by certain behaviors and people. He can express dislike of his treatment (?) He could even answer his sex if he were asked--sexuality is a different story, as I have seen debate on whether or not Data is truly capable of consent, but he is certainly aware that he is male. But, as Turing had once asked, are these machines "thinking" or engaging in some sort of "imitation game"? I, being an emotional and sentimental idiot scoffed at the idea that Data is simply mimicking behavior he sees when displaying his "personality", but a friend of mine had brought up the possibility. Does he have a "personality"? Are his actions due to his own volition and instinct, or is he simply mimicking what he believes is acceptable human behavior in accordance with his program. My friend had remarked that he believes Data is simply mimicking others, adopting the idea of companionship and talents even though he is capable of almost anything given sufficient time and effort (which is minimal compared to human counterparts). He is an apt observer and simply studies what others are like and regurgitates this into his daily way of being. And he certainly does observe, and often enjoys watching others interact, argue, gossip, etc. And then he does develop skills and social skills in accordance to the observations he gathers. So is he mimicking? But then again, aren't we all? While I am not well versed in psychology and can only account for my own experience in consciousness, I am aware that "mirror neurons" are a thing and are what assist in socialization between humans--mother and child, lover and lover, friend and friend, etc. From birth we have been shown to have the urge to "mirror" our caregivers as an act of socialization. When my cousin was born, I habitually stuck my tongue out at him, and he would do the same back to me. It forms a "bond" between caregiver and child, and is one of the first acts of socialization. We are more comfortable with people who "mirror" our behavior when we talk to them. Even my sister has once remarked that my lack of success in relationships both platonic and romantic was due to the fact that I do not instinctually mirror others and instead "do my own thing" when talking to them. This makes me not "relatable" and "unfamiliar", therefore "uncomfortable". But then the few social skills I have managed to gather, I have picked up through observation. Perhaps my observation has been a bit more of a conscious effort than others due to me not being quite neurotypical, but the same mechanisms are there. Children interact with other children and learn skills such as vocal modulation, eye contact, appropriate conversation topics, often through mimicry and exposure to appropriate behaviors. Then there's the occasional adult influence such as "no it is not appropriate to grab a woman's breasts when speaking to them" (which happens more often than you think when talking to children...) which is instructional rather than observational, but still "learned". Therefore, aren't we all just engaging in an "imitation game"? Yes and no. Because there are some instinctual factors that are encoded into our DNA that help create and shape our personalities--this causes variations between siblings who were raised in approximately the same environment. I know a set of twins, both identical and closer than anything. But one is noticeably more aggressive in her speech and stance, prefers to wear her hair purple with blonde highlights, and is bisexual. Her identical sister is a tad softer in her speech and composure, prefers her dyed solid auburn shade, and is heterosexual. They are identical twins born eight minutes apart and were raised in just about the exact same way, yet there is some intrinsic variation to their personalities that is likely more nature than nurture. Even my younger sister is blessed with the gift of perfect pitch, but I was the one endowed with musical talent (a nice irony dontcha think?). We are similar in some ways, as are the twins, but there are intrinsic differences in the personalities that is simply embedded in since conception. But does Data have such a personality? Going back to my more cynical, less emotion-driven friend and my discussion on the matter, he believes that Data does not, and this is what bars him from true humanity and "life". Perhaps he has a "sentience"--he is aware of himself and his effect on the world around him, he is aware of what he looks like in mirrors and photographs, he has a "morality" (even if it is preprogrammed, but aren't we the same?)--but he has no true, baseline "personality". Take me--at the baseline, I am hyperactive, impulsive, and easily addicted to behaviors and substances (there are probably some other traits but those are the few I know for certain are intrinsic), while my sister who is only two years younger is the exact opposite of these three states traits. But Data? My friend argued that he collects bits and pieces of persona he is exposed to that logically have a stronger "pull" in achieving his goals of seeming as human as possible and having friends, his eccentricities only coming as a result of some lacking or fallibility in his programming. And I have found myself for a long time struggling with this question... What is Data's personality described as? Loyal? Valiant? Self-sacrificing? Kind-hearted? Creative? Perfectionist to the point of occasional neurosis? Verbose? Extraverted? Ambitious? Oblivious? Honest? Curious? Courteous?* *(note, how this trait was put into him is not quite clear to me, as one episode features his mother recalling that Data was initially very rude, cold, and refused to wear clothing as he did not possess modesty. Was he taught modesty and courtesy or were they later programmed into him?) Which of these traits are as a result of mimicry? Which are as a result of his initial programming? Should we regard the traits that are a part of his programming as his own baseline personality? After all, circuit boards and microchips may program him, but DNA and RNA program us. So is Data a "person" really? Can his consciousness be really regarded as "consciousness" or is he a philosophical zombie or a hyperintelligent computer who is really good at this "imitation game"? I have much more to say on this but I apologize if any of this is incoherent. I am horrifically ill and am typing this all out on my phone in the middle of the night, so forgive me~!

[lamurdiparasian]

A Tale of Two Vector File Formats

A Tale of Two Vector File Formats

Since version 7.5, the DecoNetwork Designer has performed all of its rendering client-side to greatly improve the user experience. To help achieve this, we use SVG as our primary display format. SVG enjoys wide compatibility across browsers and most user manipulations that our designer requires can be done in real-time. If we ever run into problems, the human-readability of the format improves debugging.

However SVG is no panacea in the world of printing. This is where PDF is often preferable as a preflight format. SVG and PDF are, at their core, very different formats that have a very different target use. Here we discuss the challenges that DecoNetwork has had to overcome to reliably offer PDF as a production file format for printing, whilst using SVG for front-end display.

Color Space

One of the main limitations with SVG is its exclusive use of the sRGB color space. While it is true that SVG1.1 does actually support embedded ICC color profiles, and SVG2 supports an even wider range of managed and unmanaged colors, these features generally have no browser support. In practice, we are dealing with an unmanaged, RGB-only format. However PDFs often contain colors defined in non-RGB color spaces (for example, PANTONE spot colors, or CMYK) and we should strive to preserve this information in the upload-designer-production workflow.

With this in mind we can summarize the following objectives when dealing with PDF files:

We must support PDF as an input file format (eg, designer uploads, stock library images and so on)

Allow manipulation of imported PDF objects in the designer in real-time, using an SVG representation of those objects.

Preserve colors – including non-RGB colors – that were in the original PDF, unless they are user-modified or palette-matched in the designer.

Support PDF as an output production file format, rendering colors true to the original document or those picked/matched in the designer.

When a vector file (eg PDF) is uploaded into a deconetwork library or the front-end designer, it needs to be converted to SVG for our designer to be able to manipulate it. At a glance, it would be tempting to simply convert it with one of the many tools available, and manipulate only the resulting SVG from that point forward. Later when generating production files, we can just convert our SVG back to PDF with the same tool. This would be a relatively simple route, and a little experimentation leads us to believe that this is what some of our competitors are doing.

But alas, as mentioned earlier, when the uploaded PDF contains, for example, PANTONE® or CMYK-spot colors, the convert-and-forget approach would lose this important information and we’d be left with an RGB-only document even when we later convert back to PDF for production files. In practice, this may lead to an outcome whereby a fulfilment center prints a design on a garment where the colors look “off” compared to the file that was originally uploaded by the customer.

With this in mind, imagine we have a PDF file with the following structure:

As we can see it uses two CMYK colors and a color from an imaginary palette of spot colors. After a rudimentary conversion to SVG, we might end up with the following:

If we were to load this SVG into the designer and only consider the information it contained, we’d lose the original colors that the artist had intended to use.

Our solution to this lossy process implements a hybrid approach. Any uploaded vector is converted to an intermediate file format (DNT – DecoNetwork Template) whose objects are easily converted to SVG for display purposes but also stores the “real” color of those objects alongside the RGB representation that gets used in the SVG. This way we can build a “mapping” that we can refer to if we convert back to PDF at a later stage.

Since we didn’t want to write an entire PDF converter/parser from scratch, we build the DNT in two passes. First, we still convert the PDF to SVG using one of a handful of existing solutions. We then interrogate the PDF object structure for used colors to create the mapping which might look something like this:

Finally, we have an SVG-to-DNT converter that takes both the SVG and the above mapping to create the complete object. The DNT is converted to SVG in the designer, and any manipulations made by the user will modify both the SVG on screen and the underlying DNT.

After an product is decorated in the desinger and an order is created, we enter the production phase. If the production file format is PDF, the steps are effectively the reverse of the above process. Armed with the DNT generated from the designer, we convert it to an SVG and use off-the-shelf tools to convert the SVG to PDF. But now this PDF has only RGB colors. We have written another tool that takes the RGB mappings from the DNT and substitutes these colors directly in the PDF.

“That seems too complicated.” I hear you say. “You can just convert RGB back to CMYK with a simple formula, here’s a one I found with some googling…” Unfortunately it is not so simple. Whilst various formulae exist for remedial RGB->CMYK conversions, they are approximations at best, since RGB->CMYK is essentially a subjective conversion. CMYK and RGB colorspaces have a different gamut, so given only an RGB result, we can’t know for sure the original CMYK color from which it was generated (ie, the gamut mapping is missing). Not to mention simple formula-conversion doesn’t solve the case for spot colors. We need to, and can, do better than this.

We can visualize the PDF life-cycle as follows:

When PDFs behave badly

Occasionally we see issues with PDFs that leave us scratching our heads. In the production phase, DecoNetwork automatically captures “fatal” errors (those where a production file fails to be produced). These errors are sent immediately to our team of engineers to investigate and resolve, meaning that often problems are seamlessly rectified before the user even knew anything went wrong.

Other times, files are produced that just don’t work right. Recently a DecoNetwork client had reported that a production PDF was causing Adobe Illustrator to crash when opening. Leaving aside the general recommendation not to use AI for PDFs, sometimes you’ve got to work with the tools you have. Unfortunately AI didn’t leave any traces in its logs as to what might have gone wrong.

At first glance, there appeared to be nothing wrong with the PDF. Certainly not visually, and its internal structure appeared okay according to the various tools we had at our disposal. It would open fine in Adobe Reader, Acrobat Pro and various other open-source readers.

We were left with simply trying to track down what traits were unique to the failing PDF that didn’t exist in PDFs that worked fine. Upon inspecting the PDF in a text editor (the internal structure of a PDF is quasi-human readable), one object of interest was noted:

... 6 0 obj << /Length 568 /Filter /FlateDecode /Type /XObject /Subtype /Image /Width 1800 /Height 2000 /ColorSpace /DeviceGray /Interpolate false /BitsPerComponent 1 /SMask 7 0 R >> stream ....

  Describing what each of these tags does is beyond the scope of this article, but in short: This defines a grayscale raster image blob, using 1-bit of data per component. Since grayscale has only one component, our blob is effectively a 1-bit-per-pixel image, ie, black and white. These 1-bit rasters repeatedly showed up in the AI-crashing PDFs and were consistently absent from the PDFs that opened O.K. I suspected we had our culprit.

It is worth noting that this is a perfectly valid PDF object. However, given the size of the PDF specification, it comes as no real surprise to us that not every combination of PDF features are supported in every PDF tool (though not supporting 1 bit images – the absolute simplest type of raster, is a tad disappointing). Nonetheless the goal here is to ensure that for maximum compatibility we do not produce PDFs that contain these 1-bit objects. We instead substitute them for RGB objects (that happen to contain only values [0,0,0] and [255,255,255]). Theoretically one could “tap into” the PDF pipeline (mentioned in the previous section) at any point to substitute this object for a 24-bit RGB object.

Digging deeper, we find that the Cairo graphics library, upon which our SVG->PDF conversion partly depends, is “smart” enough to only write out a monochrome stream even if it is given an RGB stream as an input, provided those inputs contain only black and white pixels. Presumably this is to keep the file as small as possible (the above black-and-white stream uncompressed is ~9KB, the same content encoded in an RGB stream would be around 216KB). What this does mean though is our stream substitution can only be performed at the very last step, before the final production PDF is saved.

We could, alternatively, inject a single colored pixel into the otherwise grayscale stream to guarantee the stream remains RGB all the way through. This is simple and tempting, however, given the use case, we can’t help but feel introducing a new color, even if visually miniscule, could potentially spoil a production workflow.

Final thoughts

Hopefully by now you have more insight into, and have gained further appreciation of, the background processes that happen in DecoNetwork’s production file processing pipeline. At DecoNetwork we’re always adding features, and make those that are particularly experimental available to our beta testers. We encourage you to push our system to its limits and let us know the results.

from DecoNetwork Blog https://www.deconetwork.com/blog/a-tale-of-two-vector-file-formats/ Hover your mouse to Deconetwork.com from Blogger http://lamurdis.blogspot.com/2017/08/a-tale-of-two-vector-file-formats.html