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Anyone remember ENCODE? Not much junk DNA? Still not much.

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Still not much junk DNA (open access):

Conclusion

In contrast to evolutionary and genetic evidence, biochemical data offer clues about both the molecular function served by underlying DNA elements and the cell types in which they act, thus providing a launching point to study differentiation and development, cellular circuitry, and human disease (14, 35, 69, 111, 112). The major contribution of ENCODE to date has been high-resolution, highly-reproducible maps of DNA segments with biochemical signatures associated with diverse molecular functions. We believe that this public resource is far more important than any interim estimate of the fraction of the human genome that is functional. By identifying candidate genomic elements and placing them into classes with shared molecular characteristics, the biochemical maps provide a starting point for testing how these signatures relate to molecular, cellular, and organismal function. The data identify very large numbers of sequence elements of differing sizes and signal strengths. Emerging genome-editing methods (113, 114) should considerably increase the throughput and resolution with which these candidate elements can be evaluated by genetic criteria. Given the limitations of our current understanding of genome function, future work should seek to better define genome elements by integrating all three methods to gain insight into the roles they play in human biology and disease.

They seem to want to say that their bookkeeping is more important than the fact that they can’t really identify much junk DNA. (“We believe that this public resource is far more important than any interim estimate of the fraction of the human genome that is functional.”)

If they say so.

Anti-ENCODE rants from Darwin’s faithful here and here. Response.

Watching a movement self-destruct intellectually is curious. No one asked Darwin’s followers to insist that most of the human genome is junk. They could come down from the trees any time and no one will even notice maybe …

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Comments
AVS, Ok, thanks. Have a good weekend.Dionisio
April 25, 2014
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Box @ 74 Thanks.Dionisio
April 25, 2014
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That's a lovely story, but look Dio, I gave you a brief overview. If you want to talk about details then I'm sorry to say it, but you are going to need to sit down and do some serious researching on your own. To understand developmental biology you need a good background in general biology, something you simply do not have. The difficulties in studying developmental biology are compounded by the limits of our experimental model systems. Learn the basics, then you can study the detailed information that has come from studies in various species.AVS
April 25, 2014
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Dionisio, this article, about bioelectrical signals that are essential for the proper formation of the head and face in frog embryos, may interest you. Another article of interest may be the one by Stephen Talbott on context dependency. I found his commentary on a study concerning mouse hair follicles very interesting.Box
April 25, 2014
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AVS, You see, that was the kind of simple step by step info I was expecting from your lecture earlier today. You definitely made reference to a number of interesting events that take place before, during and immediately after fertilization, which seem to have implications in the cell fate determination and posterior differentiation and migration. but apparently you did not indicate at which iteration the differences appeared among the telomeres. Just mentioned some stages where some of that might occur, but left the details out. What I'm doing requires specific details, not general ideas. Can't write a program based solely on generalities. I'm currently reviewing the information gpuccio provided, which seems very good for what I'm looking for. Most textbooks out there lack the detail level I'm looking for. Also, part of the information written in most biology books is not confirmed yet. When I get this program running, i'll let you know about it, so you can look at it and give me your feedback. If you're familiar with Java or .NET C# XML XNA or Xamarin programming techniques, you could give me a hand with the actual coding too! But I'd rather take advantage of your expertise in the biology area, and deal with the programming issues alone. The hardest part for me is what seems like the easiest to you ;-) I'll write in the program credentials some note thanking all who in some way collaborated with the project. But first we have to make it work. We're not there yet. All this time I'm spending here is time I'm taking away from the project, but I wanted to take a break too. Can't sit in front of the computer all day. I can access this blog on a tablet, away from my computer.Dionisio
April 25, 2014
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AVS, Considering the explanation you provided earlier, please clarify this detail that I did not see well described in your comments: As far as you're aware of, regarding the first two cells that result from the zygote first division iteration: are they identical or different? If identical, then apply the same question to the second, third, etc. division iterations, until the first known differences appear. Thank you for your kindness to provide this information, which only you know in this thread.Dionisio
April 25, 2014
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AVS, I read the information you wrote for Dionisio, and liked what you described. However, maybe the guy was a little disappointed because you did not answer his initial most basic questions. Let me see if I can rewrite them better: 0. fertilization 1. zygote: Number of cells = 1 2. first division: Number of cells = 2 3. are they identical? 4. NO - ok, so what is the difference? respond and done. 5. Yes - identical, go to next round of division 6. Second Division: Number of cells = 4 7. are they still identical? 8. NO - ok, so what's the difference? respond and done. 9. Yes - identical, go to next division round 10. Third Division: Number of cells = 8 11. still identical? 12. NO - ok, so what's the difference? respond and done 13. Yes - identical, go to next division iteration Can you follow the above steps? I think that will make it easier for Dionisio to understand your description. Don't overwhelm the poor guy with so much information packed into one sentence or one paragraph. Go step by step, building up gradually from simple to complex, like we know evolution works, right? Thank you.TZ
April 25, 2014
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Well good for you poochy. I'm not sure why you are so proud of your lack of knowledge, especially on a topic that you constantly try to talk about. But maybe that's a quality that is revered here at UD; "the ability to talk about something you know nothing about." Yeah, sounds about right.AVS
April 25, 2014
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AVS:
Poochy doesn’t know much of anything about biology.
Thank you, AVS. Coming from you, this is one of the best compliments I ever received.gpuccio
April 25, 2014
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Poochy doesn't know much of anything about biology. Do you really think his "explanations" are reliable, especially on difficult topics, if he doesn't have a good grasp of the basics? No. I really don't care how I appear on this site because this site is a joke. I come here specifically to make fun of you guys and maybe talk a bit about biology if somebody actually starts making sense. That rarely happens though.AVS
April 25, 2014
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AVS @ 61 gpuccio humbly admits what he doesn't know, but still provides much information and advice on what he knows, always in a very respectful way. That's the main difference. Try to imitate him. He's a very passionate biology researcher. He explains difficult subjects like a professor. His friendliness is contagious. Can't find many people like him out there. Unfortunately. You may want to appear less arrogant next time, so you can get along with others. But most importantly, you should know that God loves you. I know it for sure, because God loves me, and I'm worse than you.Dionisio
April 25, 2014
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Oh I'm as chill as they come. I'm just in disbelief as to your idiocy.AVS
April 25, 2014
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AVS @ 61 Chill out buddy. You definitely need it. ;-)Dionisio
April 25, 2014
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gpuccio @ 63
Maybe you only read e-books? :)
That's exactly right! Thus I help to save the world forests, to help maintain ecological balance, so that nice guys like our buddy AVS can breathe clean air and provide us with so much detailed step by step information about fascinating biological processes that only he understands so well. Isn't it wonderful? ;-)Dionisio
April 25, 2014
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I think you guys only read picture books. =)AVS
April 25, 2014
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Dionisio: AVS says:
you know these things called “books,” I don’t know if you’re familiar with them.
Maybe you only read e-books? :)gpuccio
April 25, 2014
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Dionisio:
May God bless you abundantly.
And you.
So I guess we’ll remain ignorant for some time ahead. ;-)
We will probably survive... :)gpuccio
April 25, 2014
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Are you kidding me Dio? I took the time to write that long post and the best you can do is say I didn't explain the details? Oh but when Poochy here copys and pastes a couple things you go into full "praise the almigthy" mode. What a joke. I'm not going to write a damn book for you. I gave you a basic outline of some of the most basic events that occur in development. Now it's your turn. There's plenty of information out their that goes into further detail about what I said. You have to do some of the work too buddy. Or is that how you work, pushing of your work on everyone else. Or are you making up this whole computer science-biology story? I wouldn't be surprised. Anyways at this rate you'll have the necessary information to write your program when you're about 3000 years old. So, like I said, stick to computer science. Or get your information from reliable sources....you know these things called "books," I don't know if you're familiar with them.AVS
April 25, 2014
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Sal:
I was just giving AVS a hard time.
That's always a noble endeavour! :)gpuccio
April 25, 2014
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gpuccio @ 51 That's a remarkably insightful commentary you wrote that basically summarizes what I've started to learn in this thread. Thank you again. However, please allow me to disagree with you on one issue: apparently our buddy AVS knows a good part of what you and other science lovers don't know yet. But unfortunately he does not seem willing to share that valuable information with the rest of us here. So I guess we'll remain ignorant for some time ahead. ;-)Dionisio
April 25, 2014
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scordova @ 20 and @ 25 Thank you for the comments and the links.Dionisio
April 25, 2014
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gpuccio @ 38 Mio caro amico, mile grazie! (I don't know Italian) Thank you so much my friend! dzi?kuj? ci? bardzo, mój przyjaciel! Muchas gracias mi amigo! ??????? ??????? ??? ????! Danke schön meine Freunde! (I don't know this language) Merci beaucoup mon ami! (don't know this language either, but wanted to repeat my thanks in several languages) I don't forget you told me 'stick to biology' in another thread, in response to someone else who suggested that I get out of this blog. Today you have provided me with a substantial amount of information for me to review and study. That's very appreciated. Everyday I learn a little more. I thank God for allowing me to interact with nice friendly people like you and other folks in this blog, always so willing to share knowledge and help others who just start this 'long and winding road' of learning in the most fascinating area of science these days (in my opinion). May God bless you abundantly.Dionisio
April 25, 2014
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AVS @ 41 Apparently I had too high expectations about your promised explanations. At the end you have disappointed me. Did not provide the step by step detailed descriptions you said you were going to produce. Apparently you changed your mind about revealing the detailed information that only you seem to know? Oh, well. Your cheap marketing skills have sorta-kinda deceived me. Ok, we'll let you try again another time. But now, just go and take a brake. We're busy trying to get some real work done here. Have a good day buddy.Dionisio
April 25, 2014
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gpuccio @ 49, 50, 52 Excellent! Mile grazie! Looking into those links next.Dionisio
April 25, 2014
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AVS @ 41
Cytoplasmic determinants are present in the oocyte even before fertilization and later dictate cell fate. These cytoplasmic determinants are distributed asymmetrically in the oocyte and are involved in decreasing cell potency.
Ok, that's quite interesting. Later we'll look at this in details. But we're not there yet, so let's hold on this for now.
As cells of the embryo divide, the presence of zygotic determinants effect affect expression of other proteins according to a threshold.
Are 'cytoplasmic determinants' the same as 'zygotic determinants' in the above highlighted quotes? Just double checking. Thanks.
Cytoplasmic determinants can be mRNA themselves, actually. Protein half-lives are important in the function of some factors, keeping their distribution near their site of expression.
Ok, we can keep that in mind. Thanks. Let's move on.
I think gap gene transcription factors are an example of some of these processes, controlling gene expression patterns.
Ok, we can keep that in mind. Thanks. Let's move on.
Where the sperm enters the egg is also important in determining certain regions of the zygote. It brings about the formation of the dorsal-ventral axis and is associated with determining gastrulation.
Ok, we have to look at how the above highlighted actions occur. But that's later. Let's keep moving.
Other poles of the blastula and the fate of certain cell regions are decided in the early and late blastula stages.
Ok, show me how that highlighted (bold) action happens. Or provide a link where that's shown. Thanks. However, your explanation seems to have jumped ahead to the blastula, and has lost some granularity (details) and certain order. But hopefully we'll recover it shortly.
The location of the germ layers and the factors they secrete begins to signal cell fate determination, again using gradients of these factors to alter transcription of cells in the late blastula.
Ok, the explanation lacks details and order, but let's move on.
As the blastula develops, the cells it consists of lose their potency.
How? In simple steps, just show how that happens. Thanks. The explanation lacks step by step details.
Successive rounds of differentiation and replication lead to the formation of different cells in different regions of the embryo which in turn begin to develop more specialized structures and in the process these cells become determined.
How? Your explanation lacks a great deal of step by step details. Just point to the material where the required level of step by step details is described well. When writing programming tech specs docs I can't simply pack a bunch of steps into a couple of general statements. They'll fire me if I do that.
There’s a whole slew of protein factors involved in all this, with many studies being combined in a number of model systems.
Same problem as before. Step by step details missing from the description. This is totally unacceptable in a modeling/simulation software development project. You're fired!Dionisio
April 25, 2014
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However, in a general sense, I think that the concept that most somatic cells share the same genome remains valid.
I was just giving AVS a hard time. :-)scordova
April 25, 2014
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Dionisio: I forgot the Wiki link. Here it is: http://en.wikipedia.org/wiki/Regional_specificationgpuccio
April 25, 2014
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Dionisio: As you can see, while something is known, or hypothesized, about the epigenetic tools of cellular differentiation (but still we are at the very beginning of understanding), practically nothing is known about where the procedures are written that allow a cell to know exactly what epigenetic tools are to be activated at each step. Those procedures are probably written somewhere in the genome or elsewhere, and they must include verifications, maps and lists, and many other intelligent and functional informations. The procedural information remains still completely elusive. And it must be entirely present in the original zygote. You can also look at this wiki page for an introduction to some aspects specification. As you can see, not much is known or the real causes, and the modalities differ in different species (for example, between drosophila, where the longitudinal axis is partially determined in the oocyte) and mammals (in which that seems to happen much later).gpuccio
April 25, 2014
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Dionisio: And this one is about the possible role of transposons: http://download.springer.com/static/pdf/828/art%253A10.1186%252F1745-6150-8-22.pdf?auth66=1398605623_042a5452738fc276374c4b00dfc16637&ext=.pdfgpuccio
April 25, 2014
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Dionisio: This paper is highly tentative, but interesting: http://www.dimet.org/courses/SEMINARIO_NIAL_DILLON_27APRILE/dillon1.pdfgpuccio
April 25, 2014
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