Central Dogma: Missing, and presumed dead

_{Denyse O'Leary

May 29, 2014

Genomics, News}

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Further to “Proteome ‘more complex than previously thought’”, from Science:

“The prevalent view was that information transfer was from genome to transcriptome to proteome. What these efforts show is that it’s a two-way road—proteomics can be used to annotate the genome. The importance is that, using these datasets, we can improve the annotation of the genome and the algorithms that predict transcription and translation,” said Steen. “The genomics field can now hugely benefit from proteomics data.”

Hey, aren’t these the cement shoes of the Central Dogma? Remember when One gene coded for one protein?

See also: Information killed the Central Dogma too

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Comments

Piotr:
Sorry, Gpuccio, those threads have been buried under a heavy layer of sediments. I’ll start commenting here for want of a better place.
Best wishes on your desire to find a "better place."Mung_{June 3, 2014
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kairosfocus: Before I go away: I did not object to being called a (Neo-)Darwinist, though strictly speaking such an adjectve does not correctly describe my view of evolution if understood technically (like many others, I associate it with pan-adaptationism and underestimating the role of neutral processes). I objected to BA77's offensive and arrogant "inference": namely, that because I am a "Darwinist", my opinion on anything scientific can be ignored, for a "Darwinist" doesn't have a clue what scientific evidence is. Note that this was said at the very beginning of a discussion about physics, not biology, and that BA77 managed to derail that potentially interesting topic at once. "Darwinist" becomes a bad word if it implies contempt and not merely describes someone's theoretical position. BA77 has used the same "logic" on other occasions, e.g. dismissing any criticism of Tomkins as "Darwinist", and therefore not even worth looking at (see his reaction to wd400's example). When I spoke of an "echo chamber", I meant that regular posters tend to voice their sympathetic support even to obvious nonsense (or at least pretend they didn't hear), as long as those who spread it belong to the same camp. The most heated debates I've witnessed here were not about scientific topics but stuff like the shape of the cross in the New Testament. It's apparently more divisive than, say, guided evolution versus YEC. So long. There are reasonable people here (I'd single out Gpuccio as a particularly good discussant), so I'll continue lurking and perhaps commenting from time to time, but, frankly, I did not expect a kind of Spanish inquisition from Dionisio, of all people.Piotr_{June 3, 2014
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D: The exchange is a bit on the sad side. And Piotr at first seemed to be an exception to the run of the mill. His language clearly became quite derogatory, and the terms chosen reveal an underlying attitude of contempt. Not particularly unusual, sadly. Wish we could actually have a reasonable discussion. But I will note this, BA77 is generally courteous, though some may find his tendency to clip extensively annoying, and others may wonder about his views on Quantum mechanics and related ideas. He has his corner of the discussion and he holds his own, kudos to him. Darwinist is by no means necessarily derogatory or a dirty word, and in fact usually means Neo-Darwinist or someone who is fairly similar. IDiot is most definitely an abusive term. Echo chamber is an accusation, and one that -- given the variety of opinions in and around UD -- is not apt or helpful. Beyond, I hold no policing powers at UD. KFkairosfocus_{June 3, 2014
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Dionisio, valiant effort, but it is very rare that you will ever find a Darwinist who is actually willing to deal honestly with the evidence.,,, As I learned the hard way, You will save yourself a lot of heart ache by realizing that most Darwinists on these internet blogs are far more concerned with believing what they want to believe (atheism) than ever honestly searching a matter out and believing what is actually true. In fact, I would say that a fair amount of atheists on the internet are willing to lie to themselves and others.bornagain77_{June 3, 2014
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I'll spare you the trouble of exorcising me, Dionisio. Perhaps I have spent too much time in this echo chamber. I was curious to see what it looked like from inside, and now I know, so it's time to move on. ¡Adiós!Piotr_{June 3, 2014
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Piotr, Take a look at the following relatively recent comments copied from another thread, where you participated, but your comments were so criticized mostly due to your style. So here's a tangible example showing that I'm far from being the only one who makes the observations I made here in this thread. Actually, as you can remember, I'm probably the only one, as far as I know, who has tried to shield you from sharp criticism coming from others. So I'm surprised you're paying me back with your latest comment. Check this out and refresh your memory:
5 bornagain77 May 30, 2014 at 3:22 pm Piotr, since you are a Darwinist, I don’t think you have a clue as to what good empirical evidence really is since you have ZERO empirical evidence for Darwinism, yet you dogmatically defend it as if you did!

7 Piotr May 30, 2014 at 3:34 pm BA77, since you are an IDiot, the only thing you can do in a discussion is go off on a tangent, as in the post above.

8 bornagain77 May 30, 2014 at 3:52 pm Piotr, ad hominem does not negate your gross empirical deficiency in substantiating your Darwinian claims!

10 Dionisio May 30, 2014 at 8:01 pm BA77 Isn’t #5 an ad hominem argument? Is it right to accuse someone of doing something we also do?

12 bornagain77 May 30, 2014 at 8:31 pm No, it is not ad hominem! He is in fact a Darwinist! Though it may come off as derogatory on UD, the name is in fact a proper name for the position that he defends so dogmatically! In fact I could have called him a Neo-Darwinist, and still have been within my rights, since he defends the modern synthesis and that is the proper name for that position. He, on the other hand, called me an IDiot which is certainly a derogatory term meant to attack the man and not the argument. But most importantly, I attacked the main issue of his position in saying that he had no empirical basis. Which is certainly focusing on the argument and not on the man, whereas he refuses to honestly engage the argument and attacked the man instead!
This should be sufficient for now. The entire thread is here:
https://uncommondescent.com/cosmology/there-isnt-evidence-for-gravitational-waves-let-alone-big-claims-nature/#comment-502227
Dionisio_{June 3, 2014
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Piotr, I'm not the one having problems discussing any issues with others in any thread in this blog. If one reviews the different threads where you have been involved in, one quickly notice other participants making critical observations about your seemingly indirect style of discussion. Some folks have categorized your style more directly than others. I could ask other participants in this blog to express their opinion on their discussions with you, to see what they say. Perhaps that's one thing I should do to show you that I'm not the one having difficulties with your style. However, no style should be a problem, as long as it does not give the perception of wrong motives. That's one thing that could make others feel uncomfortable. To have the impression that the person you're having a discussion with is not sincerely trying to find the ultimate truth at the end of the discussion. To some folks that could be even annoying. To most it could be a disappointing experience. Actually, not so long ago I was kind of 'admonished' by several participants in this blog, just because I stood up to defend your participation in some discussions you were engaged in with those other folks. At the end I gave up, because they convinced me that what they were saying seemed valid. So I went back, looked at the exchange of comments between you and those other folks who rebuked me for defending your position, and I was able to see that they were right to a certain point. Your participation in the discussions did not seem to help to make the discussions flow smoothly, where both sides, while disagreeing, still had a common desire to find the ultimate truth. That's all. It's very simple.Dionisio_{June 3, 2014
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Piotr, The way you answered my questions revealed your true motives. You exposed your intentions yourself, just by the way you answered those questions. Or at least that's the impression you gave. More than once, you avoided answering simple 'yes' or 'no' questions, when the answers were simply "no, I don't know". That seems to indicate unwillingness to humbly admit lack of knowledge. I'm not playing any games here in this blog, nor have the time to do it either. But I will keep asking any questions I deem valid to have others expose their true motives for participating in the discussions. There are opposite irreconcilable worldview positions that should not be engaged in any discussion, because they simply can't have a serious discussion. All they can do is argue indefinitely, which is a complete waste of time. If both parties involved in a discussion have a common sincere desire to find the truth about the discussed subject, then the discussion can turn productive and beneficial to both sides. But if your motives are just to stay in your trench and keep defending your position, by using all kinds of slimy tricks like avoiding direct answering of questions, when the true answers might reveal weaknesses in your position, then such discussions turn into senseless arguments. Hence they better stop. Again, I will keep asking all the questions I deem pertinent. If you don't want to answer them, that's fine, just leave them unanswered. That ignoring act by itself might help reveal what's going on. But again, it's up to you to determine how the conversation will go. People with sincere desire to find the truth don't have to avoid any kind of questions, because they can answer them all. "I don't know" is a valid answer, if it's true.Dionisio_{June 3, 2014
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Dionisio, I don't think I have been patronising, interrogating, psychoanalysing or testing you. If your purpose is not to discuss things but to play poor man's Socrates with me, "reveal my real motives" (which "don't look very encouraging" to you), moralise to me and instruct me how I should have answered your clever trick questions (but I didn't, so you have to fail me), we may just as well stop conversing now. I have no time for such games.Piotr_{June 3, 2014
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Piotr @ 75
Do I know those processes? Well, I have a layman’s idea what they are. For a specialist, my “knowledge” wouldn’t count.
For me your knowledge of biology doesn't count either. I knew that. I was trying to expose your motives, your honesty, your humility, so others in this blog would be aware of it. Your answers and comments seem to reveal your real motives. They don't look very encouraging. Had you answered "No, I don't know..." then things would have looked much more different. But that was not the answer you wrote.Dionisio_{June 2, 2014
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Piotr @ 75
How am I supposed to answer “yes” or “no” to a question that is fifty-odd words long and contains several embedded clauses?
In other threads and posts you projected the impression of being very knowledgeable, lecturing others and pontificating about different subjects. What's wrong now? Did you get away with slimy techniques that allowed you to avoid confronting some subjects? You have sufficient qualifications to know how to answer that kind of question. The main part of the question was at the start: "Do you know..." the rest was related to specific areas of biology. Since you are not a biology specialist in any particular area, you should have answered "No, I don't know" right away, without hesitation. That's all. Do it better next time. Just be honest and humble. Then you should have no problems answering any kind of questions. Got it now?Dionisio_{June 2, 2014
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Piotr @ 55
It was Kepler who began to make the heliocentric model mathematically elegant.
Did Kepler use evidential observations and/or calculations to back his conclusions? Did he base his conclusions on his own personal worldview? A little of each? None of the above? Something else? What was his worldview, as far as you know?Dionisio_{June 2, 2014
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Piotr @ 75
How am I supposed to answer “yes” or “no” to a question that is fifty-odd words long and contains several embedded clauses? Do I know those processes? Well, I have a layman’s idea what they are. For a specialist, my “knowledge” wouldn’t count. The rather technical article to which I gave you a link in my answer contains a lot of state-of-art info about spindle assembly timing, and ends in a modest “we are only beginning to understand…” Why this examination at all?
You should have noticed after a quick reading of the question, that it required 'yes' or 'no' for answer. A humble, honest person would have seen the beginning of the question "Do you know..." and realize that he/she does not know the subject of the question well enough to claim knowledge. Genuine science does not claim knowledge until all the gaps have been covered. Science in general, and biology in particular, still have many gaps to cover before they can claim knowledge. They can claim partial knowledge, but not total knowledge. If the word knowledge is used without the modifier 'partial' or 'total' it might leave room for misinterpretation. I require the adjective 'partial' to be more consistent with reality. Perhaps complete knowledge will never happen, but that's beyond my understanding. This is not an examination. As I wrote before, this questioning is to expose your real intentions, your real motives. I don't like to squander my limited time arguing with fools. You have to prove to some folks in this blog that you are not a fool. You have to prove to some folks in this blog that your motives for taking part in discussions are simply to learn or to share some information you know or to discuss issues you don't agree with, but in a respectful manner. If you don't want to respect others, do not expect to be treated nicely. that won't happen. I probably still want to treat you well, even if you make fun of me, but I don't guarantee that others here will do the same. Most probably they won't. If you play games with tricky and slimy answering styles, just for the fun of it, you are wrong. Sooner or later someone will question you until you don't like it. Perhaps that has just happened today. Or maybe not yet. Respect the dignity of other persons in this or any other place. Do onto others what you would like others do onto you. That's a very simple rule that was presented by Christ to His disciples. As far as I know, it was the first time that the positive pro-active mode of that golden rule was recorded in written documents. These days many scientific papers answer a number of outstanding questions, but also raise more new questions. That's the case of the link you provided, and several similar reports, some much more recent.Dionisio_{June 2, 2014
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Piotr,
Not tonight, Josephine Dionisio. Not half past 1 a.m. Before I answer your seven questions, please answer one from me: why am I being questioned in this Socratic way?
my 7 questions in post #76 were not addressed to you. They were just a quick example showing that most scientific papers out there raise more new questions. That was all. How can you think that I could ask you questions that most scientists out there are not able to answer? That's kind of reductionist way of thinking regarding modern biology. Your poor understanding of modern biology science betrayed you - again!Dionisio_{June 2, 2014
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Piotr:
Mung, do you know a person called Sal Cordova?
Not personally, no. But I have had the pleasure of being a critic of his. He would regularly delete any of my posts from this threads. :)Mung_{June 2, 2014
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Piotr,
Not tonight, Josephine Dionisio. Not half past 1 a.m. Before I answer your seven questions, please answer one from me: why am I being questioned in this Socratic way?
Simply because I want you to prove that you are really interested in discussing, in order to find, together, the truth about the ultimate reality. The questioning is just to see what your real motives are. Have you seen anyone questioning me here in this or any blog? Can you guess why they don't question me? Because most of them noticed that I'm not fake. Are you trying to mock those who think different? Specially those who believe in the Creator of everything? If that is your intention, then get ready to be questioned more. Perhaps you did not notice it, but I got into a mild argument with other folks in this blog, because they did not like the way I stood against "ad hominem" attacks. I am for serious respectful discussions. But if you are not willing to have that kind of discussions, that means that you are not interested in the actual discussion, but in bothering the folks who are writing here. I'm definitely not a fan of people whose main intentions are to bother others who think different. All your academic knowledge and years reading and studying won't help you here, unless you are willing to cooperate by having serious discussions. Get ready for more questioning. And if you opt for ignoring the questions, it will be fine too, because remember that there are many more visitors in this blog than folks writing comments. Some of those visitors could notice what some people ignore hard questions, which probably means they are out of valid answers. So you know, either way you go, we'll be questioning. Wanna stop the questioning? Answer the questions correctly, seriously, respectfully, not slimy like some politicians do. As you can see, it's up to you to determine how things will go from here on.Dionisio_{June 2, 2014
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Not tonight, ~~Josephine~~ Dionisio. Not half past 1 a.m. Before I answer your seven questions, please answer one from me: why am I being questioned in this Socratic way?Piotr_{June 2, 2014
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Piotr @ 55
Spindle checkpoints? Why should I even attempt to “summarise briefly” such a complex technical issue in a blog comment box? Of course there are plenty of peer-reviewed publications describing it in much detail in different eukaryotes and different types of cell divisions. I’m sure you can find those publication on you own, or start here and follow the references.
Thank you for the link you provided. I have many papers to read already, most of them even more recent than the one you provided. What I want to do is chew and digest them well ;-) However, let's take a quick look at the link you provided:
Dev Cell. Author manuscript; available in PMC Jun 15, 2009. Published in final edited form as: Dev Cell. Apr 2008; 14(4): 474–479. doi: 10.1016/j.devcel.2008.03.015 PMCID: PMC2696048 NIHMSID: NIHMS95315 Linking kinetochore-microtubule binding to the spindle checkpoint Daniel J. Burke and P. Todd Stukenberg
Those look like valid credentials, right? Now, let's take a quick look at the abstract:
The spindle checkpoint blocks(1) cell cycle progression until chromosomes are properly(2) attached to the mitotic spindle. Popular models propose that checkpoint proteins associate(3) with kinetochores to produce(4) a “wait anaphase” signal that inhibits(5) anaphase. Recent data suggests that a two-state switch results(5) from using the same kinetochore proteins to bind microtubules and checkpoint proteins. At least eight protein kinases are implicated(6) in spindle checkpoint signaling arguing that a traditional signal transduction cascade is integral(7) to spindle checkpoint signaling.
(1)- how does that happen? (2)- what indicates that they are properly attached? (3)- how is that association? (4)- how is that signal produced? (5)- how des that signal inhibits anaphase? (6)- how are they implicated? (7)- how come? Left the timing mechanisms out of the questions for now.Dionisio_{June 2, 2014
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Dionisio: How am I supposed to answer "yes" or "no" to a question that is fifty-odd words long and contains several embedded clauses? Do I know those processes? Well, I have a layman's idea what they are. For a specialist, my "knowledge" wouldn't count. The rather technical article to which I gave you a link in my answer contains a lot of state-of-art info about spindle assembly timing, and ends in a modest "we are only beginning to understand..." Why this examination at all?Piotr_{June 2, 2014
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Piotr @ 55
Spindle checkpoints? Why should I even attempt to “summarise briefly” such a complex technical issue in a blog comment box? Of course there are plenty of peer-reviewed publications describing it in much detail in different eukaryotes and different types of cell divisions. I’m sure you can find those publication on you own, or start here and follow the references.
Thank you for the link you provided. I have many papers to read already, most of them even more recent than the one you provided. What I want to do is chew and digest them well ;-) My question 5 was kind of rhetorical, because I just wanted to see how you answered it, humbly, with an honest NO, or slimy, like some politicians do. Well, now we know how it went. My question #6 was not intended to be answered at all, because by answering the previous question #5 correctly (No), you were supposed to skip question #6. Gotcha!Dionisio_{June 2, 2014
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Piotr @ 55
Spindle checkpoints? Why should I even attempt to “summarise briefly” such a complex technical issue in a blog comment box? Of course there are plenty of peer-reviewed publications describing it in much detail in different eukaryotes and different types of cell divisions. I’m sure you can find those publication on you own, or start here and follow the references.
Apparently you did not read my questions 5 and 6 correctly. Question #5 required a simple 'yes' or 'no' answer. You did not answered it explicitly. After reading what you wrote, I can see that your implicit answer to my question 5 is NO, you don't know. In such case, you did not have to answer question 6 at all, but that is what you tried to do. I'm really surprised by how poorly you have done today on reading comprehension. Probably you were tired and will do much better after a good long rest. Is that what happened?Dionisio_{June 2, 2014
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gpuccio @ 61 In my comments #67 & 69 I mistakenly (again!) referred comment #59 instead of #61. Per favore perdona mio errore. No idea how I copied the wrong post numbers more than once today. Perhaps this kind of mental lapse is a sign that I should take a break too ;-)Dionisio_{June 2, 2014
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Piotr @ 68 Please, see my previous post #70. I mistakenly wrote #66 in lieu of #68. My fault. :(Dionisio_{June 2, 2014
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Piotr @ 66 I would take such comparisons as grotesque reductionist simplifications of the reality. Even in their wildest fantasy dreams, computer scientists and engineers haven't imagined anything even close to the elaborate sophistication and marvelous functionality that the biological systems present at their cellular and molecular levels. I dare anyone and their cousins, regardless of their titles, degrees, or anything else, to show me a theoretical design made by humans, where an object like the zygote has all the necessary information to become -reacting to environmental cues- a complete human being. I admit my enormous ignorance, which qualifies my to be thrown out of any discussion on science-related issues. But I dare anyone to show me any human design that can be compared to that minuscule object known as zygote. I repeat it: ANYONE! The first time I saw a medical textbook on human development, and read, with much difficulty, their description of the process that takes place during the first few days of human development, I simply couldn't believe it. I could not stop thinking about that. Back then I had to participate in technical meetings at my work, where we discussed important engineering software development issues we had to address and resolve, but my mind was completely absent from the meetings, struggling to imagine what I had read in those few paragraphs of the medical textbook, which was rather superficial, compared to the materials I'm getting now from some online journals. What had started as curiosity, turned into fascination and eventually became an irresistible obsession that made me leave my work to start studying again. When I mentioned to my colleagues what I wanted to study, some of them looked at me and told me I had lost my mind. So here I am, a mindless person, still trying to understand the processes that take place in the very beginning of human life. Now I understand much more than I did back then, but I have more questions to answer. It almost seems like a never-ending story? That's why I look forward, with great anticipation, to reading new reports from biological research, that shed more light on the wonders of biology. These are exciting days to work in biology research or to watch it closely.Dionisio_{June 2, 2014
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gpuccio @ 59
Piotr and Dionisio: I am not really sure that I know exactly what I mean! Probably, only God knows exactly what we mean. :)
Also I believe only God knows exactly what He meant when He wrote the scripts for the beautiful molecular and cellular choreographies that He is now revealing to the many talented scientists around the world, who work so hard in their research labs and who are reporting to the rest of us the wonders they are discovering these days. What we do is trying to figure out what God meant. The data avalanche is overwhelming the scientists who should analyze and interpret it, as accurately as they can, so that more effective personalized medical treatments and preventive measures can be implemented soon. These are exciting days to be in science or at least to watch it closely. Those who are on the frontline of the biological research today can have the first glance at the mind-boggling elaborate mechanisms that are appearing in front of them. But at least we can read their reports and enjoy trying to imagine the complex systems they describe.Dionisio_{June 2, 2014
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Mung @63
*sigh* Let me know if you find someone saying that.
Mung, do you know a person called Sal Cordova? http://scienceblogs.com/dispatches/2006/12/29/mikegenes-antiid-typology/#comment-37100
The issues that come up are what empirical evidence exists and which framework gives a more adequate explanation. For example, I met a couple computer science students entering junior year who were Christians. I pointed out the cell is a computer with operating systems and software and compilers. I simply posed the question, “do you think Darwinian evolution can make that? You design computer systems, do you think Darwinian evolution can make something like a computer system?” They shook their heads and laughed that evolutionary biologists actually believe that Darwinian evolution can create such systems! And I can guarantee you there ain’t an evolutionary biologist on the planet who can take first principles of information science and computer science and make a case that Darwinian evolution can account for these systems... ... For these students, there was no need to discuss peer-review, Biologic Institute, Dover, Cobb county, Kent Hovind, NCSE, or whatever. They could care less about that….For them, they are learning to design computer systems, and computer system design requires intelligence, therefore it is reasonable to them the computer systems in the cell are intelligently designed. etc.
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gpuccio @ 59
Piotr and Dionisio: I am not really sure that I know exactly what I mean! Probably, only God knows exactly what we mean. :)
Esattamente, caro Dottore!Dionisio_{June 2, 2014
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Peer-Reviewed Paper: Development Needs Ontogenetic Information that Cannot Arise from Neo-Darwinian Mechanisms - Casey Luskin - June 2, 2014 Excerpt: Jonathan Wells has published a new peer-reviewed scientific paper in the journal BIO-Complexity, "Membrane Patterns Carry Ontogenetic Information That Is Specified Independently of DNA." With over 400 citations to the technical literature, this well-researched and well-documented article shows that embryogenesis depends on crucial sources of information that exist outside of the DNA. This ontogenetic information guides the development of an organism, but because it is derived from sources outside of the DNA, it cannot be produced by mutations in DNA. Wells concludes that because the neo-Darwinian model of evolution claims that variation is produced by DNA mutations, neo-Darwinism cannot account for the origin of epigenetic and ontogenetic information that exists outside of DNA. (Read more here:) http://www.evolutionnews.org/2014/06/peer-reviewed_p_2086201.htmlbornagain77_{June 2, 2014
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Piotr:
If somebody says that any cell is a computer with an operating system, a processor, a library of programs, etc., I can only hope they don’t mean it literally.
*sigh* Let me know if you find someone saying that.Mung_{June 2, 2014
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Piotr: Take your time. Menawhile, a couple of comments: a) If our flowchart indicates that at some point one thing happens if some condition is present, or another thing happens if that condition is different, that is a decision node which refers to objective events. The condition becomes essential to the events which takes place, and the system must explain how and why the condition is present (or absent) at that time. So, flowcharts, although written on a piece of paper, are not only "convenient figures of speech", but have a definite relationship with the reality they represent (just like covalent bonds, or lines of magnetic force). Science is so important because our scientific models give us understanding and power over objective reality. It is not just a hobby to draw flowcharts or build models of electromagnetism and chemistry. b) I used "written" exactly in the same sense that we say that the sequence of a protein is written in its gene. There was no reason to equivocate. the context was (and is) very clear. c) I appreciate that you seem to have an epigenetic approach to the procedures (the rare times that you seem to acknowledge that they may exist). That's fine. I never said that they must be written in the genome, although I think that it is probably so. However, I am open to all possibilities. But I would like if you were more specific about your theories. Up to "That’s not enough to build anything. ", I perfectly agree, but then I apparently lose you. I can still maybe understand that "It’s the whole cellular context that determines how DNA is used (which is why we have different types of cells containing the same genome in a multicellular organism).", although I would like to understand better what "the cellular context" is. But what do you mean with the following? "It doesn’t matter that the transcriptome and the proteome are themselves encoded in the DNA sequence." It does matter, because we must explain why a genome which generates a specific transcriptome and proteome (in the zygote) then changes its working, and differentiates. Many times. Do you really think that that does not matter? And why? And I am completely lost at your last statement: "They must be present before anything happens to the DNA." What does that mean? Let's clarify. The zygote has the genome (the same of all the following cells, with the known exceptions). And it has a membrane, cytoplasm, and obviously a transcriptome and proteome: the transcriptome and proteome of the zygote (a super totipotent cell). Can we agree that in this situation there must be all the information, procedural or not, to guide all that will happen? Now, at different nodes, in the following divisions, new transcriptomes, new proteomes, new cells, originate. Always from the same genome, and from the original global cell context with all the changes that may have taken place in it. Are those changes that are responsible for the new transcriptomes? Probably. But what causes those changes? What are the biochemical constraints which determine the changes, which mark the future cells, which activate the right transcription factors, the right non coding sequences? From a single DNA which does not change (except epigenetically), and from a single cell context which is essentially inherited from the ovum? Where are the procedures which will give rise to more than 500 different cell types, choosing more than 500 different sets of about 400 transcription factors each out of 2000, regulating specific promoters and enhancers and not others in each cell type? If you say they are not in the genome, then please explain what cytoplasmic factors in the zygote are responsible for the ordered coordination of all those processes.gpuccio_{June 2, 2014
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