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Butterfly wing patterns emerge from ancient ‘junk’ DNA

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Re: Butterfly wing patterns emerge from ancient ‘junk’ DNA

#51
post #47

Earlier quoted context omitted.

But I can't get anything at all from the name now. BRCA1 isn't descriptive at all, but suppressBreastTumor is more helpful even it's not 100% accurate. I'd rather it be our best guess description than some random letters.

BRCA is an acronym for Breast Cancer, so we are already doing that to a large degree.

A fair point, but I think that really just lends credence to what I'm suggesting, that we expand upon that, since it isn't standardized or all that useful. If you were encountering it for the first time, what would you think WntA did?

Re: Butterfly wing patterns emerge from ancient ‘junk’ DNA

#52
post #51

Earlier quoted context omitted.

BRCA is an acronym for Breast Cancer, so we are already doing that to a large degree.

A fair point, but I think that really just lends credence to what I'm suggesting, that we expand upon that, since it isn't standardized or all that useful. If you were encountering it for the first time, what would you think WntA did?

I would look it up. Genes can encode for multiple things, so it doesn’t make sense to name them like variables, genetics is far far more complex than computer programs. Case in point, the Wnt gene codes for multiple developmental characteristics across insect groups - you can’t simply say they code for this wing protein, it does far more.

Re: Butterfly wing patterns emerge from ancient ‘junk’ DNA

#53
post #50

Earlier quoted context omitted.

What if we gain more knowledge, and this isn't suppressBreastTumor. What do you do now? As I see, the answer still cryptic name, and lookup table.

Sure, you'd expect that to happen. There are lots of interesting things you could do there, all of which are better than random letters and numbers that never change. Committees and proposals, objects and references. Things change their names all the time and society is perfectly capable of handling. Pluto isn't even a planet anymore and we all survived that. I just think we can do better than the first system we cam…

Isn’t it convenient that you could talk about Pluto without saying “PlutoTheOrbitingObject, which was known as PlutoThePlanet from 1930-2006, isn’t even a planet…”

Re: Butterfly wing patterns emerge from ancient ‘junk’ DNA

#54
post #50

Earlier quoted context omitted.

Sure, you'd expect that to happen. There are lots of interesting things you could do there, all of which are better than random letters and numbers that never change. Committees and proposals, objects and references. Things change their names all the time and society is perfectly capable of handling. Pluto isn't even a planet anymore and we all survived that. I just think we can do better than the first system we cam…

Isn’t it convenient that you could talk about Pluto without saying “PlutoTheOrbitingObject, which was known as PlutoThePlanet from 1930-2006, isn’t even a planet…”

I mean, we do almost the exact same thing with most celestial objects (ex., HUDF-JD2 aka UDF 033238.7 -274839.8 aka BBG 3179) - but the difference is they don't _do_ anything. I'm never going to write a "program" with planets, but I am interested in writing "programs" using genes. I know it's not a 1-1 example, but you know what I'm getting at.

Re: Butterfly wing patterns emerge from ancient ‘junk’ DNA

#55

Don't we have similar terminology for some of human organs. Appendix or some other organs are assumed useless. Personally I feel it's insane to call DNA or organs useless instead of acknowledging that we don't yet understand there true purpose.

Iirc appendix is now known to harbour gut microflora/bacteria when you have diarrhea, to keep them safe etc while your body clears whatever it deems unwanted

Re: Butterfly wing patterns emerge from ancient ‘junk’ DNA

#56

Earlier quoted context omitted.

Not everything serves a purpose. Onions have more DNA than humans.

Has it been demonstrated that that extra DNA has no function or are you just assuming "onions are less complex than us"?

plant like double their genome, and become stronger.

Re: Butterfly wing patterns emerge from ancient ‘junk’ DNA

#57

Don't we have similar terminology for some of human organs. Appendix or some other organs are assumed useless. Personally I feel it's insane to call DNA or organs useless instead of acknowledging that we don't yet understand there true purpose.

This term used almost twenty years ago.

Re: Butterfly wing patterns emerge from ancient ‘junk’ DNA

#58
post #44

Why don't we give genes names like functions? Seems like the whole thing might be easier to understand if we called a gene "butterflyStripeWidth" rathern than "WntA". It's like we're writing a new core library but only using obfuscated function names.

You want Wnt to be named after butterfly stripes? Last sentence below gives away wnt and lack of it leading to colon polyps/cancer. It does a million other things though. Might as well call it signaling molecule 145626.

The activation of the pathway occurs at the cellular membrane, where Wnt ligands bind to the seven transmembrane-domain protein receptors Frizzled (Fzd) and/or to the low-density lipoprotein receptor-related protein (LRP) 5/6. This interaction leads to the inhibition of the axin degradasome destruction complex, which is a multiprotein complex that controls the cytoplasmic amount of β-catenin via phosphorylation, and, thereby, triggers β-catenin degradation by the proteasome in the absence of Wnt [10]. The destruction complex comprises the tumor suppressor adenomatous polyposis coli (APC), the axin scaffold protein, and two Ser/Thr kinases: glycogen synthase kinase 3 (GSK3) β and casein kinase 1 (CK1). In the absence of Wnt ligands, CK1 phosphorylates β-catenin at Ser45 residue and GSK3β at Ser33/Ser37/Thr41 residues. Then, the β-transducin repeats-containing protein (β-TrCP), an E3-ubiquitin ligase, ubiquitinates phosphorylated β-catenin, which becomes a target for proteasomal degradation [10]. When Wnt binds to Fzd and/or LRP5/6 receptors, the Wnt/β-catenin pathway is activated and the axin degradasome is inhibited [9]. As a consequence, Dishevelled (Dvl) is activated and recruits the degradasome complex to the plasma membrane, and, thereby, promotes the interaction between LRP5/6 and axin [11,12]. Consequently, LRP5/6 is phosphorylated at specific amino acidic residues (Ser1490, Thr1530, Thr1572, Ser1590, Ser1607) [13], acting as a direct competitive inhibitor of GSK3β [14]. Moreover, inactivation of GSK3β through Akt-dependent Ser9 phosphorylation prevents the phosphorylation of β-catenin, which allows its stabilization and accumulation in the cytoplasm. Stabilized β-catenin translocates to the nucleus where it binds to transcription factors, notably T-cell factor (TCF) and lymphoid enhancing factor (LEF), TCF/LEF. This interaction displaces the co-TCF/LEF repressor Groucho, whose function under basal conditions is to compact chromatin [15]. Groucho and TCF/LEF form a multiprotein complex, which is also termed Wnt enhanceosome, that recruits transcriptional co-activators and histone modifiers such as the ATP-dependent helicase Brahma-related gene 1 (BRG1, also known as SMARCA4), cyclic adenosine mono phosphate response element (CREB)-binding protein (CBP), p300, B-cell lymphoma 9 (BCL9), and pygo [15,16]. The Wnt enhanceosome regulates chromatin remodeling and activates the transcription of β-catenin-dependent genes involved in cell growth and survival, including C-MYC, CCND1, BIRC5, and CDKN1a [9]. C-myc is a proto-oncogene that activates cyclin D1 and simultaneously inhibits p21 and p27, which leads to uncontrolled cell proliferation

Re: Butterfly wing patterns emerge from ancient ‘junk’ DNA

#59
post #54

Earlier quoted context omitted.

Isn’t it convenient that you could talk about Pluto without saying “PlutoTheOrbitingObject, which was known as PlutoThePlanet from 1930-2006, isn’t even a planet…”

I mean, we do almost the exact same thing with most celestial objects (ex., HUDF-JD2 aka UDF 033238.7 -274839.8 aka BBG 3179) - but the difference is they don't _do_ anything. I'm never going to write a "program" with planets, but I am interested in writing "programs" using genes. I know it's not a 1-1 example, but you know what I'm getting at.

Are those replacement names or additional names that point to the same underlying object? The former is much more problematic IMO.

Re: Butterfly wing patterns emerge from ancient ‘junk’ DNA

#60

Earlier quoted context omitted.

Not everything serves a purpose. Onions have more DNA than humans.

Has it been demonstrated that that extra DNA has no function or are you just assuming "onions are less complex than us"?

Ok now I'm afraid to look in that bottom drawer in the kitchen, who knows what those devious bloody alliums are up to in there.
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