The ENCODE delusion

[Blog of Reason]

Discussion thread for the blog entry "The ENCODE delusion" by Inferno.

Permalink: http://blog.leagueofreason.org.uk/science/the-encode-delusion/

 

[Vivre]

Hello Inferno,

first of all thanks for that comprehensive article that introduced a completely unknown subject to me.
It took me some hours to work it all out - am glad that I did - and hope that your current and intended investigations will spread some clarifications into the public realm.
[showmore=At this point I cannot contribute on the contains but leave some remarks on the structure]Not knowing that ENCODE wasn't intendent as elevated 'encoding' I realized pretty late into the article that it's meant as something else ... and searched for it. Maybe make the first occurence a wiki-link (http://en.wikipedia.org/wiki/ENCODE)?

The same goes with 'Evo-Devo' which I found rather funny on 1st reading, but being s.th. of real meaning.
Maybe add its written-out value in brackets behind?

And the paragraph containing the listing of 'many more identified functions' (Genomicron, 2007) I would have prefered to see as
- one function per line -
to more easily realize the single points, likewise allow relaxed comparison among them[/showmore]
Your suggestion to add 'Epigenetics' as possible reason also came to my mind

[joke]
Concluding my own assumption I'd suggest to call the non-coding DNA - MEPSGKJIC :
~ maybe erewhile proved success genes kept just in case ~
This would make it pretty obvious to the puplic that the scientists still have no clue at the given moment
[/joke]

And apart from fighting for facts a philosophical note arose in my mind:
:mrgreen: if 80% of the universe turns out to be dark matter why shouldn't this be found reflected in the genom as well?

again THX ... also for showing me a serious issue these creationists try to base on

greets ~ Vivre

edit: added MrGreen

 

[Inferno]

Thanks for the reply, Vivre.

Not knowing that ENCODE wasn't intendent as elevated 'encoding' I realized pretty late into the article that it's meant as something else ... and searched for it. Maybe make the first occurence a wiki-link (http://en.wikipedia.org/wiki/ENCODE)?

My bad. Yes, I should have done that. But what with all the links already in the article, I simply missed it. And the Evo-Devo one too. Additionally, I was writing this with people in mind who might already have heard of the two. Again, not such a clever assumption on my part.

And the paragraph containing the listing of 'many more identified functions' (Genomicron, 2007) I would have prefered to see as
- one function per line -
to more easily realize the single points, likewise allow relaxed comparison among them

There are three reasons I did not do this:
1) They're like that in the original and I like to keep the original formatting as much as possible.
2) Had I spread them out, the paragraph would have been three or four times as long... not something I'd find appealing.
3) The packed writing screams, at least to me, "there's so much". As in "there's so many possible functions", whereas a long-ass list would have seemed thin.

I guess it's a preference of style...

if 80% of the universe turns out to be dark matter why shouldn't this be found reflected in the genom as well?

Ha!

Well Dark Matter doesn't have "no function" in the same way that Junk DNA does. But yours was a joke, right? It's difficult to judge, we need those damn sarcasm-tags.

 

[forgotten observer]

we need those damn sarcasm-tags.

Inferno Correct me I I'm wrong here but don't we already have them? Observe tuxbox's post here
http://www.leagueofreason.org.uk/viewtopic.php?f=10&t=11555
(Put your mouse over the text)

 

[Inferno]

Thanks, Forgottenobserver. For me, only the codes that are in button format are implemented, so I completely missed that.
Yay for sarcasm!

 

[Prolescum]

That tag shouldn't be used, as it will in all likelihood disappear; the tag's existence is as an implementation example.

 

[Vivre]

I'm glad the hints were appropriate, knowing you rather address towards the boardmembers at the moment ... but aiming towards the public on the long.

As for the respect of keeping quotations as pure as possible I too go with you. If I would be on topic I would likely just quick-glance over that addressed paragraph, for knowing its contains more or less. But for me it was just a pain to try to extinguish what of it was pregnant and what was additional source info.
At that point I simply made my own adapted off-line version of your article to comfort myself. (unfortunately the blog side doesn't supply a print view as alternative)

But as for 'The packed writing screams' I'd like to show you that in this case it would still stay a remarkable block of info but a thin list
[showmore=just to visualize]Examples include buffering against mutations (e.g., Comings 1972; Patrushev and Minkevich 2006)
or retroviruses (e.g., Bremmerman 1987)
or fluctuations in intracellular solute concentrations (Vinogradov 1998),
serving as binding sites for regulatory molecules (Zuckerkandl 1981),
facilitating recombination (e.g., Comings 1972; Gall 1981; Comeron 2001),
inhibiting recombination (Zuckerkandl and Hennig 1995),
influencing gene expression (Britten and Davidson 1969; Georgiev 1969; Nowak 1994; Zuckerkandl and Hennig 1995; Zuckerkandl 1997),
increasing evolutionary flexibility (e.g., Britten and Davidson 1969, 1971; Jain 1980; reviewed critically in Doolittle 1982),
maintaining chromosome structure and behaviour (e.g., Walker et al. 1969; Yunis and Yasmineh 1971; Bennett 1982; Zuckerkandl and Hennig 1995),
coordingating genome function (Shapiro and von Sternberg 2005),
and providing multiple copies of genes to be recruited when needed (Roels 1966).[/showmore]
Yes, sarcasm-tags might really be of need - I added a MrGreen above :mrgreen:

 

[Inferno]

OMIFUCKINGGOD!!! This post was sourced over at Genomicron!

I'm famous! Muahahahah!

So excited! XD

Hey, does that count as a citation?

 

[Aught3]

Nice one Inferno, it was a hell of a post too.

 

[he_who_is_nobody]

OMIFUCKINGGOD!!! This post was sourced over at Genomicron!

I'm famous! Muahahahah!

So excited! XD

Hey, does that count as a citation?

:shock:

Congratulations! This is wonderful news.!

 

[he_who_is_nobody]

Once again, Inferno, you have raised the bar for this blog and forum. I thank you for that and am honored to be apart of it.

 

[Inferno]

See, now I can't tell if you're making fun of me or not.

 

[he_who_is_nobody]

See, now I can't tell if you're making fun of me or not.

I am not. I mean everything I have said.