fredreload

That my algorithm is great? What do you guys want?

Immortality means you have as much time to waste as possible, money is not a problem

Cell differentiation is driven by things like chemical gradients

https://en.wikipedia.org/wiki/Cellular_differentiation#Mechanisms

 

(Note that lizards don't actually grow back a fully functioning tail but, rather, a tail-shaped lump of flesh and bone.

From your Wikipedia link I've read about the transcription factors for IPSC programming Oct4, Sox2, and Nanog proteins are involved, actually 4 proteins for the Nobel prize winner. Now I've made a conclusion that transcription factors and microRNA actually does the same thing here. In which both of them does the same thing in gene silencing and gene activation. Now if microRNA also plays an important role in cellular differentiation, why isn't it mentioned in the link? That's my first question.

Second question, can epigenetic eplains which cell turns into a muscle cell and which cell turns into bone cell, if so, how?

P.S. No zombie dream = =

P.S. Kids, microRNA is important

If I am a lizard and my tail got cut off, how do I know what to grow back?

After making a time consuming compression algorithm, as always. I being to wonder if it is worth it to trade off time for money. We all work, I know, and as much as I would like immortality to work, it seems it requires a bit more time. So at a realistic point, if immortality is not yet achieved, is it worth it to trade time for money?

Is there a better way for sorting binary numbers Strange?

You would, I assume, also need to know what values were swapped at each pass. There is, in general, no algorithm for reversing a sort other than either recording the original order or recording what was done at each step of the sort.

 

But well done for choosing a bubble sort if you want a slow algorithm.

(Although it is one of the fastest algorithms on some parallel architectures.)

Thanks man, you are awesome, sorry about the challenge I made, I might have to start my calculation right after Big Bang, well, reversing is my specialty

P.S. This is one of a few sorts I can do correctly in an exam

Alright I got a question, assuming you have an array, 67142 that is sorted into 12467 from Bubble sort, how do you get the original sequence 67142 from 12467? Can you reverse run the program?

P.S. Wait never mind problem solved, beat that Strange , you need to know how many pass you've ran though https://en.wikipedia.org/wiki/Bubble_sort

Is there a way to use a huge amount of time for a decent compression on bits?

Even if you had the structure (e.g. via crystallographic approaches), figuring out their function is still a long. loooong process. Or take proteomics, we routinely look at hundreds or thousands of proteins and monitor their expression under many conditions. Still, we generally rely on our old-school knowledge of known biochemical pathways to make sense out of the patterns. Again, what is missing is not the patterns, but figuring out what they mean. Even if you know the general role of a protein (say, vesicle trafficking) it will fulfill many different roles depending on what they particular cells needs to be done. E.g. it could direct signaling vesicles, or nutrients, or direct lipid genesis etc. Now you have thousands of them of which you vaguely know they roles or not at all.

It requires extensive manipulation and many many experiments even on simple cells to use that information to tease out potential functions.

 

Edit: the movie is a cartoon we have no way of getting that. It is one of the grails in structural biology, where we use e.g. femtosecond X-ray crystallography to try to capture confirmational changes. There are only a handful of examples where we might have seen something, and it took years in each case (not to mention a massive X-ray source). And this is only for minute changes (say, photoactivation of a molecule), nothing like a complex folding.

 

But to re-iterate, while structure can help in figuring out function, it is a non-trivial process. And even if you know that that enzyme specifically binds a certain substrate, you still do not know the physiological role. I.e. when does it do that, to what reason, and what are the consequences if does not do that. The reason being that all the proteins are connected via massive networks. If you poke a whole in one area, it may be caught by something else entirely, so you do not see a phsyiological reaction. Or the opposite may happen, where it actually affects a distal part of the network, which leads to entirely unexpected results. Again, the limiting factor are not the measurements as such, but good theoretical framework or models which helps us to understand these vast amount of data. This is where bioinfomratics originated. And while there have been approaches (such as in the biochemcial modeling frameworks) it is still very limited and barely works on the single cell level. Anything beyond that tend to be empirical models (if at alll).

Right, I was looking into the attosecond laser and its detection on molecular changes before I look into laser spectroscopy. I guess I had my hopes up thinking the whole thing can be visualized

P.S. I thought it would be possible to track each protein using a visual analysis program on the animation, but you say acquiring such an animation is not possible at this point then I guess we'll have to wait and see

The part about the visualization technique 0:22~0:40, year 2030

 

 

We can use RNAseq do examine gene expression already. Also, knowing the sequence of amino acids in a protein doesn't mean you know its 3D structure (assuming it's fixed, as many proteins fold differently in different environments - hence the environment plays a role in how the protein functions) , so no, simply knowing a particular amino acid sequence is expressed does not mean you know what the protein looks like, what it does, or how different variants of the gene result in differently functioning proteins.

 

Furthermore, plenty of functional genomic regions are non-coding, regulatory regions. Expression/translation of these genes doesn't necessarily tell you about their function.

Right well I'm thinking of creating an animation that looks like this(man I feel like a kid asking for candy), I'm not sure how accurate this animation is. The amino acid sequence is not the only thing observed, but how it folds into a 3D shape and how it's used as well as its functions the whole picture. You can let me know if that is not possible with the current technology

You are still looking at the wrong/easy thing. We have a somewhat decent grasp to look at molecular composition (at least if we ignore dynamics for the most part). But the problem is that changes in expression tells you little what they actually do. The reason being that they are not activated exclusively by some event, but many are induced by a multitude of intra-and extracellular signals. And your repeated claims of imaging still does not make any sense as you do not add functional information to the mix.

Well, my idea is about observing everything from DNA to mRNA, what gene expression is is the rate of a certain strand of DNA copied to the mRNA, if it is not expressed it is not copied. We agree that this messenger RNA is passed to the bacteria ribosome and eventually synthesize the protein there, then we trace this protein to see what gets developed all using hyperspectral imaging at real time like an animation. Sounds like science fiction, well at this point it might be. And if simply synthesizing the protein with messenger RNA in the ribosome is not the whole picture then you can explain to me what is missing. Well this is all theoretical, I respect you for doing the actual work on the bacteria and you are free to tell me what I should be looking for

Hmm, you got 4 neucleotides and around 20 amino acids, from these number you can predict just about all the instructions given to a cell unless you are doing something like 20 factorial. I always thought you'd be able to track the DNA code, how it becomes mRNA and eventually protein in the ribosome based on these amino acids. As to how the instructions differ for a bacterium, I can't really say, I'd trace the mRNA, amino acid, and how it programs the protein to react. As for how DNA works for cell division like from zygote to blastocyst you'll have to check the gene expression and essentially the instruction that signal human shape to take place and differentiation of tissues. I always felt like this is kept secret or that my understanding of Biology isn't that great but clearly each cell has a different gene expression and something is coordinating these gene expressions to form the human shape and instruct cell differentiation. Arete probably has a better understanding of this

P.S. Well but, I bet you are not examining the bacteria at a molecular level->hyperspectral imaging

Well the point is from zygote to human takes cellular divisions and as it grows the gene expression is constantly changing, which part of the DNA shows which part of the body is being developed. And yes there would be microRNA involved as well as how it is instructed to perform the task. Nevertheless, once the human shape takes place I feel that it would be harder for us to find the DNA that instructs how cell should be differentiated to take the human form. For a grown up human the shape doesn't change anymore, so I think less can be observed in comparison to the developmental stage. Unless you have regeneration property and you observe how the body parts regenerate with microRNA

You make that sound significantly easier than it would actually be to do.

Well, laser scanning is a powerful technique, but to observe the DNA might require laser spectroscopy or using dyes. I am not sure about the resolution for such a technique not to mention observing a specimen in vitro. The hard part is to get the observation technique, after that we can probably start with some smaller specimen

P.S. The only thing I could find is hyper spectral imaging, with some shading applied it could be quite convincing

Pretty far. In fact, we do not have clear approaches to that end. Or rather, we have figured out a lot of things that don't work well over the last 10-15 yearxps. So any prediction would be a wild guess.

What I can think of is to observe the earlier stage of human development, zygote->blastocyst->body forming using a non-intrusive laser scanner. The thing is I'm not sure if this would be ethical, you'll need external birth for this. Then you get a 3D view of all the molecular mechanisms involved. Once you get this you can replay it however many times you want, I think, theoretically. We can't do it yet because there isn't external birth and I doubt anyone is going to volunteer for this

A species of jellyfish gets younger.

That is really cool. I would like to know how the cells revert back to its original state without cell division. I mean even for IPSC cell it needs to divide a few times before specialized cells become stem cell

P.S. Wait never mind, I looked up transdifferentiation and that kind of explains it

P.S. Gonna have to check the miroRNA on this one

Well what I had in mind was a film from a friend named "The Curious Case of Benjamin Button", got me thinking if you can actually program the DNA to reverse growth. Cell goes through mitosis to create a cell that is a few days younger

I understand some people have their genome fully sequenced, but that doesn't mean we understand what the genome does. So when is it that we will finally be able to know that a particular sequence represents height or something else having the genome fully decoded?

Right, make sense

Imagine all your body functions reversed and you grow younger each day, how does that even work, you would be self sustaining and outputing rice and bread for 80 years? What do you guys think? Anyway I got it from Family Guy

I caught a cold from my co worker, is that considered a bio weapon, I was sick for three days. What other types of bio weapons are there?

So after watching this video, I'm not quite sure how specific microRNA is produced for the cell type. It's like skin cell only produce skin cell regulatory microRNA and muscle cell only produce muscle cell regulatory microRNA, but what causes the RNA Polymerase 2 to select and produce the microRNA needed for the cell type?

P.S. We're getting real close guys

A mitotically-produced cell is the same age as the cell it cloned from.

 

The thing about stem cells is not that their age/youth is the distinctive property but their ability to make any type of cell. They still get 'old'.

This article suggests that IPSC cell from an old donor has its molecular clock reset, including all DNA damages and telomere length. I'm not sure how he reprogrammed the IPSC cell, the lizard regeneration technique is thought to achieve with microRNA while IPSC cells I've heard about is derived from transcription factors. You think these adult stem cells can also be reprogrammed in the same way to get young stem cells? Well, it is true that the lizard's blastema might not be derived from the IPSC cells, no offense really

P.S. Ah, I found it, what you've mentioned is the adult stem cells found among normal cells, I'm guessing these can also be reprogrammed

Not if the 'new' part was mitotically produced from cells which are at the current level of senescence of the organism; they are the same age. The tails are actually regenerated from cartilage cells; no bone is regenerated. As far as I know, cells must be meiotically produced to put a cell at age zero i.e. start again. Cloning doesn't do this.

Well but, the new part consists of progenitor cells or stem cells in which they call it the blastema that eventually becomes the new limb, it doesn't make sense that these stem cells are at the same age as the specialized cells. They might be mitotically produced from the nearby cells, which are specialized cells, but they are still stem cells, so this makes it confusing as to whether it is an age 5 stem cell or an age 0 stem cell. Either that or they could be transformed to stem cells from these specialized cells, their age should be 0 right?