/sci/ - Science & Math

>>14813745
Come on /sci/, this is an interesting topic.

>>14813745
I too think this is an insanely interesting topic. But I don't know shit about it.

Know nothing about this topic but it seems very interesting

>>14814393
>>14814400
Retarded dumbfucking nigger zoomers.

>>14813745
>How do our cells know to grow into 5 prongs at the end of longer prong?
I've actually shown that there have to be two different unit cells intersecting each instance of H.

>>14813745
Probably something to do with the so called "junk DNA" ie the 98% of our DNA that isn't protein coding. It somewhat appears to alter the pacing of the protein coding genes. This has earth shattering implications though, because gain of function mutations in coding DNA would therefore very often simultaneously require random mutations in the "junk" DNA that describes when or in what order to use the other mutations. As a rough analogy if you're building a complicated lego set a random tweak to the design would require a random tweak to the instruction manual at the same time for the tweak to be utilized. It doesn't seem naturally feasible.

The cells don't know shit. Molecules do not think. It's a stochastic system of forces and particles and the most likely outcome is a hand with 5 fingers.

>>14813745
>Okay, how do the morphogens know where to go, what concentrations to be in where, etc?
It's all rather complicated.
To start the whole development process off, you need some initial asymmetry in the distribution of proteins or RNAs in the zygote. There are all sorts of ways this can be acheived. In Drosophila, if I remember right, there are gradients of maternally expressed proteins in the egg chamber which bind to transmembrane proteins in the zygote. Some organisms use the same sort of cellular machinery which allows single-celled organisms to become mobile to accumulate certain mRNAs at one side of the cell, but where they will sit, blocked from translation by some kind of interfering RNA until such time in the developmental process that something appears which sequesters the interfering RNA and allows translation to proceed.
This initial assymetry means that different proteins are present in student parts of the developing embryo, which starts long, complex chains of signalling molecules and feedback loops, which are rarely fully understood.
If you read up on this stuff, even with the best studied developmental programs there will be certain parts in the textbook account where it says something like 'somehow this causes localised translation of protein xyz, but fuck knows how'.

>>14814786
I think this is the most important problem in biology, yet we know fuck all about it. We all learn in high school biology that DNA is a blueprint for organisms, but it's not. It's a blueprint for proteins. There is no static blueprint for organisms. The blueprint is an emergent dynamic process of self-regulating signalling pathways which conspire in some insanely complex, miraculous way to produce an organism with a particular form.

>>14814860
>I think this is the most important problem in biology, yet we know fuck all about it.
Nah, we know plenty, and a fuck load more than we knew just twenty years ago. It's just that there's still so much more to learn.

>>14813745
>How is DNA, a molecule which only codes for proteins, responsible for this?
You know 99% of the DNA that is supposedly "junk DNA"? It's not. That's how.

>In 2012, a research program called the ENCODE project concluded that
>around three quarters of the noncoding DNA in the human genome did undergo transcription and that
>almost 50% of the genome was available to the proteins involved in genetic regulation such as transcription factors.

>>14814931
So this black box of junk DNA somehow codes the morphology of organisms, but you havn't explained how.

>>14814951
We know a lot about what non-coding RNA does. Some of it forms part of the ribosome - the structure which is responsible for actually translating coding-RNA. Transfer RNAs are another non-coding RNA involved in this process - they bind amino acids and present them to the ribosome for translation.
Several different kinds of ncRNAs work to regulate the translation of proteins by binding to mRNAs and either blocking their translation or catalysing their degradation. One of the ways in which those RNAs are stopped when they are not needed is via the transcription of yet another type of ncRNA which competes for binding with them; preventing them from repressing translation.
Others bind to chromatin; the stuff which packages DNA in the nucleus. This changes chromatin conformation and makes particular genes more or less open for transcription.
All these different ways to affect the level of transcription and translation of different genes is what allows the morphogens to 'know where to go', as OP asked.
Some of it probably is just junk, though.

>>14815005
I feel like at each molecular level, we're still left with a "how does x "know" to do y?" question. How does ncRNA "know" to regulate the translation of certain proteins in specific cells but not others? Without a central blueprint for the development of an organism, I don't see how these signalling pathways can coordinate with each other.

>>14814951
> DNA somehow codes the morphology of organisms
Not 100% sure, there's going to be way more stuff than just DNA. DNA is only 1 part of the system.
>DNA is replicated before cell division, so the same genetic material can pass from parent to offspring.
>mom and dad and grandma and granddad have 2 hands and 5 fingers each
>DNA passed along to offspring to have 2 hands and 5 fingers.
>This trait was great and the one that survived and procreated
>Anon you didn't tell me how
Anon, monkeys have 5 fingers. Some geckos have 4 or 5 fingers. The encoding of this trait into a mammal DNA likely happened millions of years ago. And just being passed along.

>>14815090
>The encoding of this trait into a mammal DNA likely happened millions of years ago
Two hands and 5 fingers is not encoded in DNA. That's the problem. You're working under the misconception taught in high school biology that DNA is a "blueprint" for organisms. It's not. There's no gene or sets of genes which say a human should have 5 fingers.

You're thinking about it wrong.
There is no "coding" happening. Atoms have certain ways of forming molecular bonds with other atoms. Strings of atoms bounce against each other to form different structures. These structures then bounce against other structures in a process called natural selection. The structures that don't get broken up, and can go on to copy, permeate. But all of it is just atomic interactions.
Your body, and the bodies of all the lifeforms on earth, are directly implied by the laws of physics in the same way the motion of the planets are.

>>14815109
Brilliant explanation anon. You should publish this in Cell so scientists can create life saving gene therapy using your illuminating analysis.

>>14815087
The RNA doesn't 'know' to do anything, it does what it does as a function of it's structure. What decides whether it does its thing is whether it's present in a cell (or a region of a cell) and whether or not it's sequestered by interactions with some other RNA or some protein.
I get what you're saying, but the retarded and dismissive replies of other anons do have a kernel of truth in them. There's no blueprint, because this all is not appearing from scratch; it's part of a long, evolutionary process. Parts of the signalling pathways used in making this all work are extremely conserved - you see the same pathways and the same specific types of interactions between different motifs used for all sorts of different purposes in cellular regulation, because the bafflingly complex processes we see today are the results of these different pathways being repeatedly tweaked and gradually coopted to different purposes. So, the process by which your neurons 'know' to grow axons in one specific direction is remarkably similar to the way that yeast cells 'know' where to grow mating projections.

>>14815151
He's asking how do cells or proteins "know" what to do. They don't, not any more than hydrogen and oxygen "know" how to form together to form water. That isn't how it works. The reason that the DNA produces the RNA to produce the proteins that form into a 5 fingered hand is because that is what is directly implied by the laws of physics and those combinations of atoms.

>>14815421
>>14815399
>ackshually molecules can't know things
I can't tell if this is wordcel pedantry or actually deficient verbal intelligence.

>>14815399
I'm not claiming they "know" things. I'm asking for an explanation that DOESN'T involve them "knowing" things. You're missing the entire point of my question and this thread is just over your head. Please leave and stop contributing bullshit truisms everybody already understands.

>>14815486
Did you read past the first clause of my post, you mong? I am the only person in this thread actually trying to address your question.

>>14815552
You've explained that morphogenesis is the result of signalling pathways. I already understand that. I'm asking how these processes work.

>>14813745
Concentration gradients. Everything is concetration gradients. That is literally all developmental biology is. Concentration gradients of transcription factors.

Put "simply", genes determain which proteins are made, and proteins determain the shape and nature of the cell. They do this via the cytosceleton, basically various shapes and sizes of protein tubes and chains.
So what a cell is shaped like, and how soft/har/squishy/dry it is is all dependant on which of the genes are expressed (so proteins are made from them) and which are not.
Expression of a gene is determained by transcription factors (gene + trancription factor = transcription = mRNA, mRNA + spliceing + translation = protein)
Now what matters is where each transcription factor may be at what concentration. This will be determained by a cascade, started by maternal mRNA.
I'm shit at explaining things, i hop this wasn't too retarded of a way of putting it.

>>14815578
How do these concetration gradients form in the first place? How is a certain hox gene expressed in cells in one part of the embryo, but not the other? How do variations in gene expression which produce transcription factor gradients occur in different cells at different parts of the developing organism?

>>14815621
>How do these concetration gradients form in the first place? How is a certain hox gene expressed in cells in one part of the embryo, but not the other?
It's maternal cells passing mRNA to the germline cell, the oocyte. So eggs actually aren't symetrical. I'm shit at drawing, but i gave it a try. Now this is way oversimplyfied, this is a vast field of research, there are several types of maternal mRNAs we get, and there is also asymetrical cytosceleton due to maternal cells creating concentration gradients.

>>14815621
You need an initial asymmetry.
You have a zygote. It divides in two. If the distribution of proteins or RNAs in the parent cell was not uniform, the two daughter cells now have differing protein and/or RNA contents, and now you're set up for differing chains of signals to take place in different cells.
Pic related is a diagram of a Drosophila egg chamber - the coloured bits at the front at the actual egg; the reat are maternal cells. This egg has not been fertilised yet, but the different colours represent concentrations of mRNA - much of which is transported into the cell from the adjacent nurse cells. Before this egg is fertilised, it's already set up so that the daughter cells of the zygote will have differing concentrations of proteins - setting off the chain of events that lead to different development patterns for different cells.

>>14815621
atoms have different areas on their outer "surface" - the layer that interacts with other atoms - that have positive and negative electrical charges, and these charges dictate how two or more atoms interact with each other. This is what the other anon you've been arguing with is talking about when he says everything obeys the laws of physics. Atoms are an insanely complicated set of tinkertoys, they link together in strange and interesting ways and become molecules, which do some even weirder things when they interact with each other. It all depends on the placement and orientation of the positive and negative electrical fields. Imagine building a crazy framework contraption with magnets all over it pointing every which way, now build a million of them and throw them all in a big box together. They're going to stick together in some places and repel each other in others, and to think that you could get some sort of repeatable result that you could use to make machines that dependably perform functions, that just boggles my mind.

These vids are old but still the best I've seen, hope they help: https://www.youtube.com/watch?v=7Hk9jct2ozY

>>14815657
>>14815667
Thanks, these are helpful.
>>14815678
You're a retard.

>>14814876
what a... dishevelled diagram

>>14816102
It's rare I lament I lack of a like button on 4chan.