Central Dogma: Missing, and presumed dead

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

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

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. KF kairosfocus

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

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

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://uncommondesc.wpengine.com/cosmology/there-isnt-evidence-for-gravitational-waves-let-alone-big-claims-nature/#comment-502227

Dionisio

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Piotr @ 68 Please, see my previous post #70. I mistakenly wrote #66 in lieu of #68. My fault. :( Dionisio

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

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

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.

Piotr

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

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.html bornagain77

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

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

"This remarkable process of cellular computation implies that cellular materials can show a primitive intelligence," the team writes in Nature. - When slime is not so thick

Here we show that this simple organism has the ability to find the minimum-length solution between two points in a labyrinth. - Intelligence: Maze-solving by an amoeboid organism

Mung

Piotr,

To be continued (sorry, I’m a little busy tonight).

Sure, take a break buddy. Have a good night sleep and get some rest tomorrow. If you want to come back, get ready to discuss, because the discussion is just starting, the subject is very important and not simple at all. This time I want to get to the bottom of this discussion, while trying our best to communicate well. At some points I may have to consult my friends -biology scientists who work in research at universities in North America and Europe- but I will try as much as I can, not to bother them with questions. However, scientists from your university in Poznan are welcome to join our discussion if they want to. Agree? Thanks! Dobranoc! (here they say 'the brown nuts') ;-) Dionisio

Piotr and Dionisio: I am not really sure that I know exactly what I mean! Probably, only God knows exactly what we mean. :) gpuccio

Gpuccio:

What does that mean? If we humans can model what happens as a complex flowchart, it’s because the events in the flowchart take place. A flowchart has nodes, which represent decisions made according to logical evaluations.

But the flowchart is something that we draw on a sheet of paper. It's the way we understand and visualise the process, just like family trees are useful diagrams representing relationships, not real objects in the real world. Living things reproduce and population sometimes diverge to the point of speciation. They "form a tree" only in a highly abstract sense, when we model their history. Likewise, physicists speak of "lines of magnetic force" and chemists of "covalent bonds", and they can visualise them as geometrical objects, but of course they realise such "lines" and "bonds" are convenient figures of speech.

Now, I am not saying that there is any “central agent” (where did you take that idea?) who takes the decisions. The flowchart simply represents events that take place. The reasons for those events can even be “dispersed in the chemistry of the cell”, but that does not mean that they do not exist. Even if they are “dispersed”, that is no reason not to try to understand where they are “written”. I believe you are equivocating my term “written”. It means that, if certain different events take place at different times and in different conditions, but according to a repeated pattern, there must be some objective configuration in the genome, or more generally in the cell, that explains that ordered series of events. That’s what I call “written procedures”. They must be there. Chemistry alone can do nothing to decide the transcriptome of a B lymphocite out of the generic genome.

So you use written metaphorically and then accuse me of equivocating on that? OK, I don't think its "written" in the DNA, to begin with. Let's suppose we can synthesise a fully sequenced genome. That's not enough to build anything. 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). It doesn't matter that the transcriptome and the proteome are themselves encoded in the DNA sequence. They must be present before anything happens to the DNA. To be continued (sorry, I'm a little busy tonight). Piotr

Piotr: "If the procedure is written somewhere, we should be able to see it." Why? There are certainly so many things that exist, and that we are not yet able to see. gpuccio

Piotr,

Only Gpuccio knows exactly what he means, but I believe we are able to communicate.

Your answer to my questions 2, 3 and 4 could be interpreted as "No, I don't know" - is this correct? If you don't know exactly what he meant by 'procedure', 'written', 'intrinsic', 'extrinsic', then how can you write absolute statements about gpuccio's definitions? It doesn't seem like you are able to communicate well with gpuccio, because he has explained several concepts that you don't seem to understand well. Understanding each other doesn't necessarily mean agreeing with each other. But in your case the understanding part seems poor. Or at least that's the perception outside observers might get. Dionisio

Piotr,

I hope so. If the procedure is written somewhere, we should be able to see it.

You failed to answer correctly the first question, buddy. Your original sentence was not a scientific statement at all. We don't know everything in this field of science, therefore we must watch carefully what we say or write about it. Absolute statements demand absolute knowledge, which you or no one else possesses in this particular case. Even your answer to my first question lacks qualifications to be considered scientific. You seem to know much more than I do, so you should have been able to figure it out yourself, or could have asked someone at the university in Poznan, where you work, maybe they could have helped you to answer my first question. It's pretty obvious. Actually, I'm surprised you answered the way you did. If we have not seen them yet, and we know we are still discovering things as we dig deeper, and we are still answering outstanding questions, while new questions are popping up, and we know we don't understand well many things, then we don't have any rights to imply that gpuccio's procedures don't exist anywhere. That's an absolute statement about something you are not absolutely certain. Hence, that sentence does not qualify as scientific, because it's misleading. In addition, since you're not absolutely certain about the meaning of gpuccio's term 'procedure' then you can't say much about its possible existence. First you must know what the Italian Doctor means by 'procedure' within the discussed context, although he has explained it to certain point in some of his postings, but you can always require additional clarification of the term, if it's not sufficient clear to you. Humility is an important requirement for a scientist to be genuine. However, apparently you're not a scientist, and I'm not a scientist either. Fortunately most true scientists are humble enough to admit their lack of absolute knowledge on certain areas of their endeavors. The rest of us must crave for that virtue too. Rozumiez teraz? Bardzo dobrze! Dionisio

Oh no, Kepler was a Creationist who understood science as a way to understand God's Creation. Joe

1. Is that a scientific statement? I hope so. If the procedure is written somewhere, we should be able to see it.

2. Do you know exactly what gpuccio means by ‘procedure’? 3. Do you know exactly what gpuccio means by ‘written’? 4. Do you know exactly what gpuccio means by ‘explicit’ or ‘implicit’ procedures?

Only Gpuccio knows exactly what he means, but I believe we are able to communicate.

5. Do you know the mechanisms that determine the precise timing for the centrosome segregation, so that the spindle apparatus works correctly in the intrinsic asymmetric mitosis, thus leading to the appropriate fate determination, differentiation and migration, for every cell during the initial stages (first few days) of human embryonic development, starting at the zygote? 6. If your answer to question 5 is yes, then can you provide a brief summary of those mechanisms, or provide links to recognized peer-reviewed publications, where those mechanisms are described in detail?

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.

7. When your ‘rodak’ Nicolas Copernicus wrote his heliocentric theory, did he base his conclusions on solid evidences he had observed and worked on, or just on speculations that conformed to his worldview?

A little bit of this and a little bit of that. For example, he was still under the spell of the ancient Eudoxan model with transparent crystal spheres (hence "perfect" circular orbits, corrected with the use of epicycles). There was no observational justification for any such things (not to mention a physical theory to account for them quantitatively) -- just a philosophical tradition going back to ancient Greece. It was Kepler who began to make the heliocentric model mathematically elegant. Piotr

Piotr at #33: I am rather surprised of your statements here. You say:

There is no procedure written anywhere. What we humans could model as a complex flowchart or an algorithm is actually dispersed in the chemistry of the cell, with no central agent to control its execution.

What does that mean? If we humans can model what happens as a complex flowchart, it's because the events in the flowchart take place. A flowchart has nodes, which represent decisions made according to logical evaluations. Now, I am not saying that there is any "central agent" (where did you take that idea?) who takes the decisions. The flowchart simply represents events that take place. The reasons for those events can even be "dispersed in the chemistry of the cell", but that does not mean that they do not exist. Even if they are "dispersed", that is no reason not to try to understand where they are "written". I believe you are equivocating my term "written". It means that, if certain different events take place at different times and in different conditions, but according to a repeated pattern, there must be some objective configuration in the genome, or more generally in the cell, that explains that ordered series of events. That's what I call "written procedures". They must be there. Chemistry alone can do nothing to decide the transcriptome of a B lymphocite out of the generic genome.

DNA sequence doesn’t do anything by itself. It contains no program or procedure; it’s only data.

Yes, and so? Procedures are data too, until they are executed.

Life is a complex quasi-periodic process which uses DNA as a memory.

That seems really meaningless.

The memory is used to store recipes for structural, catalytic, signalling and regulatory molecules — inherited recipies that have worked in the past.

OK. So, in our genome we have those recipes. For n molecules, some of them structural, other regulatory, and so on. Those recipes are the same in all cells. So, how do those recipes generate 500 different and complex transcriptomes, in definite order and with definite form? If you have a list of 500 ingredients, how do you get 1000 different recipes from it? Do you just shake the list and hope for a good result?

The memory is replicated and passed on from cycle to cycle, making sure that the process is repeated as faithfully as possible.

What do you mean by "cycle"? What governs each individual "cycle"? Please, be specific. Remember, the memory is the same in all cells, and the transcriptomes and proteomes are different in each cell type.

Proteins are chemicals. They don’t think and they don’t carry out commands. They are not intelligent nanorobots moving smoothly along an assembly line. They move about and fluctuate due to Brownian motions. They interact with other molecules in ways determined by physics and chemistry, and not because a sequential algorithm tells them to execute “step number 8453?.

Excuse me, but this is really silly. It's the last version of the famous, and infamous, "it's all chemistry" triteness. OK, you are a linguist and you certainly use words better, but the concept remains silly just the same. Of course "proteins are chemicals". Of course "they don’t think and they don’t carry out commands". Whoever said anything like that? Proteins obey chemical laws. They move about and fluctuate due to Brownian motions. They interact with other molecules in ways determined by physics and chemistry. What a brilliant discovery that is! But, if they "execute “step number 8453?, whatever it is, the reason is that some sequential algorithm (IOWs, some ordered series of events) creates the circumstances that force them, by the laws of chemistry, to execute step number 8453. You know, molecules are not there in the wild executing step number 8453 all the time, just because chemical laws require it. Step number 8453, whatever it is, is a very definite circumstance which happens at a very definite time in a very definite cell. Why? That's the reason why a B lymphocyte is not a fibroblast. Because step 8453 takes place in the B lymphocite, but not in the fibroblast. That step, the fact that makes it happen in the B lymhocite, and all the 8452 steps that preceded it, and the many that will follow it, are what I call "the procedures". And believe me, they are written somewhere. gpuccio

Piotr @ 33

There is no procedure written anywhere.

1. Is that a scientific statement? 2. Do you know exactly what gpuccio means by 'procedure'? 3. Do you know exactly what gpuccio means by 'written'? 4. Do you know exactly what gpuccio means by 'explicit' or 'implicit' procedures? 5. Do you know the mechanisms that determine the precise timing for the centrosome segregation, so that the spindle apparatus works correctly in the intrinsic asymmetric mitosis, thus leading to the appropriate fate determination, differentiation and migration, for every cell during the initial stages (first few days) of human embryonic development, starting at the zygote? 6. If your answer to question 5 is yes, then can you provide a brief summary of those mechanisms, or provide links to recognized peer-reviewed publications, where those mechanisms are described in detail? 7. When your 'rodak' Nicolas Copernicus wrote his heliocentric theory, did he base his conclusions on solid evidences he had observed and worked on, or just on speculations that conformed to his worldview? No need to rush in order to answer the above questions. You may take all the time you want to. Also, remember that "I don't know" is a valid scientific statement, which demonstrates humility, a virtue that is not abundant in this world. Thank you. Serdecznie pozdrawiam. Dionisio

Mung: You are conflating different levels of organisation. An ant colony is more than a set of n ants, and a neural network is more than a set of n neurons. Even water is more than a large collection of H20 molecules. Interactions between components are an essential party of any system (without them there is no system in the first place). Now if you claimed that even a single neuron did "computations", I would agree. It's the function of a neuron to do just that -- it is a cell specialised in processing and transmitting signals. But is it "a computer"? I would hesitate to say so, because I don't care for stretched metaphors. 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. If they explore the metaphor still further for rhetorical effect and say, "A cell is a computer and we know that all computers have to be built and programmed by highly intelligent beings, so it must be true of living cells", they've lost me. Inferences from an analogy are not valid. It's like saying that since stars are thermonuclear reactors, and since the only other thermonuclear reactors we know of are human-made (and small, and very imperfect), an efficient thermonuclear reactor, such aa a star, can only be the work of a superintelligence. Has anyone ever seen a molecular cloud organise itself into something that even the human genius can't imitate? There are also people who claim the the whole Universe is one humongous computer. Fine, but by doing so they dilute the semantic content of the word "computer" homeopathically. If it can mean anything complicated, it means nothing in particular. Piotr

Basic Concepts for Neural Networks Mung

Piotr:

Sorry, but the cell is not a neural network either.

Are you sure? What are neural networks composed of and where do neural networks come from, if not from cells? Are you one of those epi-phenomenalists? ;) Take a bunch of cells that have nothing remotely similar to a neural network in them and place them together at just the right time and in just the right place and in just the right relationship to each other using random modifications and natural selection and 'voila', you have a neural network? Seriously? Isn't it more reasonable to believe that there's nothing really new in neural networks, that cells have been doing this on their own for millennia? Mung

Piotr, you are really on a roll today.

Sorry, but the cell is not a neural network either.

So? Relevance please. I'm not engaging in ad hominem and perhaps you could respond by not engaging in non sequiturs. Fair enough? Why are you being so dismissive? Have I treated you badly somewhere? If so I apologize. 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.

So I tried to engage you on the issue of processes in the cell, the topic you address in your post @33. I've raised a number of relevant points which you haven't even bothered to attempt to respond to. Yet you even agree that processes exist!

It’s the biochemical processes taking place in the cell that “read” the data and make use of it, but the analogy between those processes and a computer is a poor one.

So let's try a different approach. In what sense do you say these processes exist? Do they only exist as analogy or metaphor? If so, how is it that they manage to have a predictable physical effect? How is it that they manage to have a repeatable predictable physical effect? Don't you realize that by taking the position that these procedures are not "written down" anywhere that you're appealing to magic? And gpuccio is asking, if they are written down, where are they written? And if not in DNA, then where? And if not in DNA, how are they heritable? You are obviously an intelligent person. You can see the implications. But you should also face them and deal with them. If your current paradigm has problems providing answers, then perhaps there is something wrong with your paradigm. Peace. Mung

Piotr, the cell is a miniature automated factory. Joe

Mung:

http://en.wikipedia.org/wiki/Wetware_computer

Sorry, but the cell is not a neural network either. Piotr

What you are doing, Piotr, is concentrating on the hardware, not the processes. gpuccio is asking about the processes. You claim there are none. I offer the testimony of what ought to be a recognized expert in the field, and you poo-poo it by mistaken analogies. The point here is on computation. The cell is, quite literally, performing computations. Now if perhaps you'd care to say something about the nature of computation and offer something relevant to whether or not cells do or do not carry out computation?

Computation is a process following a well-defined model understood and expressed as, for example, an algorithm, or a protocol.

A computation can be seen as a purely physical phenomenon occurring inside a closed physical system called a computer. Examples of such physical systems include digital computers, mechanical computers, quantum computers, DNA computers, molecular computers, analog computers or wetware computers.

http://en.wikipedia.org/wiki/Computation http://en.wikipedia.org/wiki/Wetware_computer Note the reference section of the second link for a review of Bray's book. Mung

Mung: #41 Here I part ways with Bray. A computer processor (or one of a battery of parallel processors) performs a sequence of explicit instructions stepwise. A living cell does not do "the same thing" #42 Analogy. Figure it out yourself. Piotr

Piotr, speaking of trajectories, why the flight away from data and biology into physics? Mung

Piotr, "There is to begin with, the matter of computation. In a circuit board or microchip, sets of logic elements linked in precise networks perform defined logical processes, repeating the same simple steps over and over again. The same thing happens in a living cell..." - Dennis Bray (p. 27) "The central thesis of the book - that living cells perform computations - arises from contemporary findings in the biological sciences, especially biochemistry and molecular biology. It is a leitmotif of systems biology, although the philosophical ramifications of that new discipline are rarely expressed." (p. xi) Mung

Information Theory, Evolution, and the Origin of Life - Hubert P. Yockey, 2005 Excerpt: “Information, transcription, translation, code, redundancy, synonymous, messenger, editing, and proofreading are all appropriate terms in biology. They take their meaning from information theory (Shannon, 1948) and are not synonyms, metaphors, or analogies.” http://www.cambridge.org/catalogue/catalogue.asp?isbn=9780521802932&ss=exc A New Design Argument - Charles Thaxton Excerpt: "There is an identity of structure between DNA (and protein) and written linguistic messages. Since we know by experience that intelligence produces written messages, and no other cause is known, the implication, according to the abductive method, is that intelligent cause produced DNA and protein. The significance of this result lies in the security of it, for it is much stronger than if the structures were merely similar. We are not dealing with anything like a superficial resemblance between DNA and a written text. We are not saying DNA is like a message. Rather, DNA is a message. True design thus returns to biology." http://www.arn.org/docs/thaxton/ct_newdesign3198.htm "And at this point, strangely enough, the discovery of DNA, which is so widely thought to prove that life is mere chemistry, provides the missing link for proving the contrary. That the formation of a DNA molecule is embodied in the morphology of the corresponding offspring, assures us of the fact that this morphology is not the product of a chemical equilibration, but is designed by other than chemical forces." Michael Polanyi, “Life Transcending Physics and Chemistry,” Chemical and Engineering News 45 (August 1967): 66, 55-66 Assessing the "Algorithmic Origin of Life" (Paul Davies' Recent Paper) - December 18, 2012 Excerpt: It is the functionality of the expressed RNAs and proteins that is biologically important. Functionality, however, is not a local property of a molecule. It is defined only relationally, in a global context, which includes networks of relations among many sub-elements,, One is therefore left to conclude that the most important features of biological information (i.e. functionality) are decisively nonlocal. Biologically functional information is therefore not an additional quality, like electric charge, painted onto matter and passed on like a token. It is of course instantiated in biochemical structures, but one cannot point to any specific structure in isolation and say "Aha! Biological information is here!",,, ,,,For example, mechanical stresses on a cell may affect gene expression. Mechanotransduction, electrical transduction and chemical signal transduction -- all well-studied biological processes -- constitute examples of what philosophers term "top-down causation", where the system as a whole exerts causal control over a subsystem (e.g. a gene) via a set of time-dependent constraints. http://www.evolutionnews.org/2012/12/assessing_the_a067541.html Dichotomy in the definition of prescriptive information suggests both prescribed data and prescribed algorithms: biosemiotics applications in genomic systems - 2012 David J D’Onofrio1*, David L Abel2* and Donald E Johnson3 Excerpt: The DNA polynucleotide molecule consists of a linear sequence of nucleotides, each representing a biological placeholder of adenine (A), cytosine (C), thymine (T) and guanine (G). This quaternary system is analogous to the base two binary scheme native to computational systems. As such, the polynucleotide sequence represents the lowest level of coded information expressed as a form of machine code. Since machine code (and/or micro code) is the lowest form of compiled computer programs, it represents the most primitive level of programming language.,,, An operational analysis of the ribosome has revealed that this molecular machine with all of its parts follows an order of operations to produce a protein product. This order of operations has been detailed in a step-by-step process that has been observed to be self-executable. The ribosome operation has been proposed to be algorithmic (Ralgorithm) because it has been shown to contain a step-by-step process flow allowing for decision control, iterative branching and halting capability. The R-algorithm contains logical structures of linear sequencing, branch and conditional control. All of these features at a minimum meet the definition of an algorithm and when combined with the data from the mRNA, satisfy the rule that Algorithm = data + control. Remembering that mere constraints cannot serve as bona fide formal controls, we therefore conclude that the ribosome is a physical instantiation of an algorithm.,,, The correlation between linguistic properties examined and implemented using Automata theory give us a formalistic tool to study the language and grammar of biological systems in a similar manner to how we study computational cybernetic systems. These examples define a dichotomy in the definition of Prescriptive Information. We therefore suggest that the term Prescriptive Information (PI) be subdivided into two categories: 1) Prescriptive data and 2) Prescribed (executing) algorithm. It is interesting to note that the CPU of an electronic computer is an instance of a prescriptive algorithm instantiated into an electronic circuit, whereas the software under execution is read and processed by the CPU to prescribe the program’s desired output. Both hardware and software are prescriptive. http://www.tbiomed.com/content/pdf/1742-4682-9-8.pdf bornagain77

Unguided evolution cannot be modeled, Piotr. And unguided evolution can't even account for DNA. BTW if a metaphor is inescapable then it most likely isn't a metaphor. Joe

Piotr: It’s the biochemical processes taking place in the cell that “read” the data and make use of it, but the analogy between those processes and a computer is a poor one. I partly agree with the blurb you linked:

You're basically right. It's not really analogous to a sequential computer. It is more analogous to a CNC machine. No less astounding. http://en.wikipedia.org/wiki/Numerical_control Vishnu

Piotr: Proteins are chemicals. They don’t think and they don’t carry out commands. They are not intelligent nanorobots moving smoothly along an assembly line. They move about and fluctuate due to Brownian motions. They interact with other molecules in ways determined by physics and chemistry, and not because a sequential algorithm tells them to execute “step number 8453?.

All true. Except only part of the truth. Consider Dawkin's "Weasel" program. Despite a random number generator as the source of variation, the result always ends up as "METHINKS IT IS A WEASEL" within a fairly small number of iterations. Why? Because the randomness is highly constrained. While the proteins are most definitely molecules, they have a highly specific shape that, in relation to other "keyed" proteins, yields highly specific functions when they encounter one another. Proteins may bounce around with a cell with Brownian motion, but they do so with blazingly fast speed, such that proteins encounter their keyed proteins fast enough to allow their specific function to be performed in a timely manner. It's the "software" that makes the difference; that defines the constrains that shapes all the flurry of randomness into extremely specific function. The "software" in this case being the particular codon sequences in the DNA that produce proteins with their specific molecular shapes that constrain the randomness with their particular function. The source of the highly constrained boundaries is the source of controversy between those who "see" intelligence as the source and those who don't- the source of the software. Hand-waving statements that they are "determined by physics and chemistry" is no more pertinent or explanatory than saying computers operate determined by "physics and electronics." True, but hardly a full or useful description of what occurs. Vishnu

Even if DNA is “only data” it doesn’t follow that it contains no program or procedures, wouldn’t you agree?

It's the biochemical processes taking place in the cell that "read" the data and make use of it, but the analogy between those processes and a computer is a poor one. I partly agree with the blurb you linked:

Dennis Bray taps the findings of the new discipline of systems biology to show that the internal chemistry of living cells is a form of computation.

... as long as it's understood that we are speaking figuratively, and a metaphor is only a metaphor. There is no actual processor and no actual algorithm. Piotr

Mung: I am not contradicting myself. We can model things, but our models should not be confused with reality. You can model the motion of a canonball mathematically and calculate its trajectory. Where are the equations written? In a handbook of physics, perhaps, but canonballs don't read handbooks and don't solve the differential equations we write for them. The "laws of physics" are generalisations formulated by humans. They reflect our current understanding of reality, which is inherently provisional and incomplete. We update our knowledge, change out models, sometimes have to pull down the whole theoretical edifice and build a new one from sctratch. Cannonballs don't care and nobody informs them of our paradigm shifts anyway. Piotr

Piotr:

DNA sequence doesn’t do anything by itself. It contains no program or procedure; it’s only data.

Even if DNA is "only data" it doesn't follow that it contains no program or procedures, wouldn't you agree? Your computer hard drive contains "only data," as does your computer's RAM, but that data includes many programs and procedures. And programs and procedures can be distributed, processes can run in parallel, and there doesn't have to be a central agent controlling them all. Agreed? Mung

Piotr:

There is no procedure written anywhere. What we humans could model as a complex flowchart or an algorithm is actually dispersed in the chemistry of the cell, with no central agent to control its execution.

Again, you seem to claim both that no procedure exists anywhere and that procedures do exist, but they are distributed. Whether there is a 'central agent' to control the execution seem to be irrelevant, wouldn't you agree? Wetware: A Computer in Every Living Cell Mung

Piotr, you appear to be contradicting yourself.

There is no procedure written anywhere. What we humans could model as a complex flowchart or an algorithm is actually dispersed in the chemistry of the cell, with no central agent to control its execution.

Life is a complex quasi-periodic process which uses DNA as a memory. The memory is used to store recipes for structural, catalytic, signalling and regulatory molecules — inherited recipes that have worked in the past. The memory is replicated and passed on from cycle to cycle, making sure that the process is repeated as faithfully as possible.

Mung

Gpuccio:

Still, Piotr has recently stated that no “explicit” procedures are needed. I answered that, in post #108 here: https://uncommondesc.wpengine.com.....-part-two/ but he has not commented further. I still would like to know where he thinks the procedures are written, explicit or not.

Sorry, Gpuccio, those threads have been buried under a heavy layer of sediments. I'll start commenting here for want of a better place. There is no procedure written anywhere. What we humans could model as a complex flowchart or an algorithm is actually dispersed in the chemistry of the cell, with no central agent to control its execution. DNA sequence doesn't do anything by itself. It contains no program or procedure; it's only data. Life is a complex quasi-periodic process which uses DNA as a memory. The memory is used to store recipies for structural, catalytic, signalling and regulatory molecules -- inherited recipies that have worked in the past. The memory is replicated and passed on from cycle to cycle, making sure that the process is repeated as faithfully as possible. Proteins are chemicals. They don't think and they don't carry out commands. They are not intelligent nanorobots moving smoothly along an assembly line. They move about and fluctuate due to Brownian motions. They interact with other molecules in ways determined by physics and chemistry, and not because a sequential algorithm tells them to execute "step number 8453". Piotr

RodW: In no way I was implying that you should agree with waht I was saying. I just profited of something that you said, and with which I did agree, to express my ideas. :) I am aware that gene regulation has always been a part of the scenario, but one thing is to reason in terms of promoters and enhancers, or of single transcription factors, another thing is to address the problem of a general informational plan, what I call "the procedures". There has been a gradual shift from a purely mechanistic approach to a more integrated view, but I think that the official scientific position is still very reluctant to admit a very simple truth: the whole differentiation process, and its coordination and control, which allows a same genome to produce hundreds of sophisticated specialized transcriptomes and proteomes, is still completely elusive, not only because we don't know the details (which is not in itself a problem), but because we have really no idea of where the complex procedures that must be there, somewhere, really are. There are those who simply deny that those procedures exist. They seem to think that things just happen for a lucky series of feedbacks, which in some way makes the genome capable of taking the correct path towards each type of cell, of tissue, of organ, of form. But anyone who has even the simplest understanding of how informational systems work can easily realize that such a position is utter folly. When a cell has to activate a definite group of transcription factors, let's say 400, out of the 2000 which are available in its genome, and it has to activate them in definite order and quantity, and regulate them and everything else by complex networks like nuclear RNAs and peptides, alternative splicing, epigenetic processes, post translational modifications, and so on, and those processes are different and specific in each cell type, and in each phase of a single cell type, then it is very easy to understand that what I call "the procedures" is a lot of explicit information, and that it must be coded somewhere. I believe that understanding where and how those procedures are coded should be the absolute priority in this moment. After all, the continuous accumulation of ever growing datasets is making that understanding a little bit easier. gpuccio

gpuccio

I think you express very well the problem in your last post.....The problem is: “where is it”? The whole subtext of the “central dogma” question is that there has been a general confidence that information was mainly, if not almost exclusively, in the protein coding genes.

Thanks but I don't quite agree with some of what you say. They've known since the 1960s that genes are controlled by non-coding regulatory segments and in the 1970s when they showed that human and chimp proteins are almost identical they concluded that all the differences must come from regulation. Since the 80s many in 'EvoDevo' have asserted the notion that most of animal evolution is due to changes in protein regulation. But its true that new levels of regulation seem to be constantly turning up! Yesterday I read a review article that mentions that protein translation in the cytoplasm can effect transcription in the nucleus. There seem to be a lot of people here who are very interested in this stuff but don't have any 'formal' training. I just don't think its possible to pick it up in bits and pieces. I strongly recommend that those interested buy an advanced text like Molecular Cell Biology by Lodish and read it cover to cover. There are great courses on Youtube like Eric Landers at MIT but I don't think that's advanced enough for people here. RodW

Are you aware of any theory explaining this accent difference? Could it be that she has a genetic predisposition for languages that I lack? Or could it be that Slavic (particularly Polish) women are better at speaking foreign languages? Thank you.

There are some results showing that women in general (not just Polish ones) have better bilingual skills than men. This may have to do with the fact that the performance of language-related tasks seems to be more strongly lateralised in men and involves more bilateral activation in women (for the same reason brain damage is less likely to affect women's linguistic abilities). There might be an evolutionary explanation of that: if early human communities regularly practised linguistic exogamy (with men taking wives from a different tribe, with a different native tongue, as come societies of the Amazon still do), this could have led to a selective pressure favouring greater plasticity of language-learning skills in women (they had to learn their husbands' languages but not vice versa). But it's only a guess: I'm not aware of any formal studies confirming it. Needless to say, the effect is statistical and doesn't have to be confirmed by each individual case. Piotr

RodW: I think you express very well the problem in your last post. Central dogma or not, it is obvious that the information for all that will happen (with possible modulations from the environment) is already there, in the zygote (or however in the initial cell for unicellular beings). We could just say that it flows from "where it is" to "where it must go". That is a very general way to describe things, but it should be correct. The problem is: "where is it"? The whole subtext of the "central dogma" question is that there has been a general confidence that information was mainly, if not almost exclusively, in the protein coding genes. But the simple truth is that such a view cannot explain the "procedures": how those genes are used and regulated in so many specific, finely tuned ways, especially (but not exclusively) in metazoa. That important problem has become specially relevant now, when we are beginning to have a general map of transcriptomes and proteomes, not to speak of the whole epigenetic-friendly trend. I hope that the old attitude, of simply pretending that there are no procedures written anywhere, will become sooner or later obviously irrational to all, and not only to us in ID. Still, Piotr has recently stated that no "explicit" procedures are needed. I answered that, in post #108 here: https://uncommondesc.wpengine.com/intelligent-design/is-functional-information-in-dna-always-conserved-part-two/ but he has not commented further. I still would like to know where he thinks the procedures are written, explicit or not. A very good starting point could be your comment: "In a way you could say that this and other so-called violations of the dogma aren’t really violations, they just reflect the fact that information coded in the DNA is coded in many layers or dimensions." It's exactly those "layers or dimensions" of the coding, which IMO will certainly in many ways include non coding DNA, which can allow some understanding of cell differentiation and function, a topic of some importance, I believe. And a topic of great relevance for the ID debate, given that it is about coded functional information. :) gpuccio

Dionisio

Now, do those findings you mentioned, relative to the Nature links posted in my comments #3, 4 & 8, conflict with the so called ‘central dogma’ of biology?

That's an interesting question which would probably require several pages of discussion. The Central Dogma states that information flows from DNA to protein, and not in the reverse direction. None of the supposed examples of violations of the dogma I've seen have included RNA editing, but it seems to me it should be included. On the other hand, the enzyme that edits RNA is coded for in the DNA, and the place and time of its expression is controlled by DNA. In a way you could say that this and other so-called violations of the dogma aren't really violations, they just reflect the fact that information coded in the DNA is coded in many layers or dimensions. As an aside I'll say that I was a Biochemistry major for 4 years and took grad classes and was in grad school for 6+ years and in all that time I heard the phrase 'Central Dogma' mentioned once- in an undergrad class. Most scientists don't concern themselves with it. You wouldn't even call it a theory..its a sort of generalization. I think I recall hearing that the word 'dogma' was meant a bit tongue-in-cheek ( mistake earlier - my friend worked on Shaker not ADAR. ADAR is the enzyme) RodW

#24 RodW

I think the point of the Nature paper from 3 years ago was that they used data from the human genome along with new info on proteins that were directly sequenced and found an unexpectedly large number of genes edited in humans. I can look up stuff if you have more questions!!

Thank you for the explanation, which seems to answer the questions in my comments 3, 4, 8. Now, do those findings you mentioned, relative to the Nature links posted in my comments #3, 4 & 8, conflict with the so called 'central dogma' of biology? Dionisio

#21 BA77 Thank you for sharing that interesting information. I'm sure many talented folks who write in this blog can understand that report much better. But I definitely enjoy anything I can get out of it. Your comments usually have interesting links and quotes. Thank you for the effort you make to compile that information and share it here. Many interesting reports -like the one you have shared with me- will keep appearing in the scientific media at an increasing rate, as the research technology turns more precise and efficient. These are exciting times for scientists and for the rest of us who follow closely the results of their research work. Still much remains unknown. For example, in this case the report says: “However, the mechanism of ncRNA-mediated protein sequestration is not understood at the molecular level.” That’s why we should look forward, with much anticipation, to the news coming out of the labs, which will shed more light on the amazing biological systems we are so eager to understand. Currently I'm busy -sweating and struggling- while trying to understand the mind-boggling mechanisms associated with the precise timing of the centrosome segregation for the effectiveness of the spindle apparatus operating on the intrinsic asymmetric mitosis during the initial stages of human embryonic development. I take frequent breaks to rest. Sometimes during those breaks, I check to see what's going on in this blog. There are many interesting areas in biology that I would like to read about, but can't do it, because time is very limited and goes by very fast, I'm a slow reader, my reading comprehension is rather low, and my IQ score is similar to my age ;-) That's why I enjoy reading the free abstracts of some papers that are behind paywalls. Those compacted summaries are sufficient to excite my imagination. ;-) Rev. 22:21 Dionisio

Piotr, Thank you for sharing that detailed information on the story behind that part of the English language. I could not describe that well even my first language (Spanish) ;-) Now, let me take advantage of this opportunity to ask you a language related question about spoken accents. My wife and I have very different accents in English, even though we both came together to the US and have a comparable knowledge of the language (well, perhaps she knows it slightly better than I do). Could it be that the noticeable accent difference has to do with our first languages being so different too? There are sounds in Polish languages that I still can't pronounce correctly, and probably never will. However, my wife speaks Spanish without accent. She can pronounce all Spanish sounds like any person in Madrid, where we lived before moving to the US. She even claims that Spanish is much easier to learn than other languages she knows or is familiar with, including French, German and English. Are you aware of any theory explaining this accent difference? Could it be that she has a genetic predisposition for languages that I lack? Or could it be that Slavic (particularly Polish) women are better at speaking foreign languages? Thank you. Dionisio

Dionisio I think ( not sure) that editing was first discovered in protists and later fruit flies. The guy I knew worked on the ADAR gene in drosophila which is edited. I'm not sure when the first human ( or vertebrate) edited gene was discovered. I think the point of the Nature paper from 3 years ago was that they used data from the human genome along with new info on proteins that were directly sequenced and found an unexpectedly large number of genes edited in humans. I can look up stuff if you have more questions!! RodW

Dionisio:

However, these days most potential readers wouldn’t have noticed the difference between “its” and “it’s”

Actually, "these days" are not so different from "days of yore". The possessive pronoun its became acceptable in literary English about 1640, well after Shakespeare's death. Until that time, the possessive form of it had been his (of Old English origin, and Shakespeare's regular choice), or the periphrastic genitive of it. Its was an innovation, formed on the analogy of "Saxon genitives" like William's. The spelling it's was very common until about 1800, when the variant without the apostrophe began to prevail and came to be regarded as standard. Piotr

Piotr, An "Edit" button would be a nice feature. I could use it many times ;-) However, these days most potential readers wouldn't have noticed the difference between "its" and "it's". As an English language specialist you know that better than I do. Przyjemnego 'weekendu' ! Dionisio

Dionisio, this may interest you: Does a Kitchen Sponge Have a Function? - May 30, 2014 Excerpt: A recent paper in Nature shows that there is a small, non-coding RNA, transcribed from DNA, that acts as a "protein sponge" to soak up the excess. It can then "squeeze" the extra proteins back out for work, when conditions are favorable.,,, This is no ordinary sponge. It has a "well-defined" structure that is "well-tuned" to sequester proteins.,,, the molecule works in a "cooperative, well-defined and regulated manner," as opposed to the "random fashion",,, The authors were surprised to see such finely tuned design in a simple molecule whose only role is to act as a sponge. Each binding induces a conformational change, so that proteins are bound and released in sequence.,,, http://www.evolutionnews.org/2014/05/does_a_kitchen086171.html bornagain77

Dionisio, I noticed the superfluous apostrophe the moment I was clicking on "Post". Unfortunately, there's no "Edit" button. Piotr

Piotr, malutka poprawka:

Is it junk news? It may have some space-filling and structural functions, but it’s sequence doesn’t matter.

Is it junk news? It may have some space-filling and structural functions, but its sequence doesn’t matter.

Dionisio

Is it junk news? It may have some space-filling and structural functions, but it's sequence doesn't matter. Piotr

You forget Acartia, this is a "News" post so there is no requirement for the post content or title to match the linked article. Such minor details would just get in the way wd400

So, what dogma is being busted her? Rather than using the genes to identify the proteins, they are using the proteins to identify the genes. Acartia_bogart

# 12 RodW

RNA editing has been known about for about 15-18 years. I knew someone who worked on it in 1999

That's interesting. Thank you for sharing that information. Back in that year you mentioned (1999) I was busy working overtime on a software development project for engineering design applications on PC. My wife was busy working on software development for business applications on large IBM mainframe systems. Back then the only editing I knew was to write or maintain programs written in C language. My wife edited her programs written in COBOL, DB2, CICS, etc. My children knew more biology than I did back then. Today they are both doctors in medicine, so they still know more biology than I do (well, many people out there know more biology than I do). Ok, enough digression, let's go back to the subject. If, as you stated, RNA editing has been known for so long, then why did a respected peer-reviewed publication like Nature dared to publish 3 years ago the two articles I mentioned in my comments # 3 & 4, which clearly give the impression they were kind of surprised? Does that make sense? Also the Nature article linked in my comment # 8 seems to present a similar dilemma, even though it was written just over a year ago. Can you explain this apparent contradiction? Thanks again. Dionisio

RodW- Just because we know of RNA editing doesn't mean unguided evolution didit. Joe

edit (third-person singular simple present edits, present participle editing, simple past and past participle edited) To change a text, or a document. Mung

Dionisio RNA editing has been known about for about 15-18 years. I knew someone who worked on it in 1999 RodW

I thought this thread was going to be about the fast & convergent evolving to avoid parasitic fly crickets in Hawaii chirp chirp. Talk about Dogma Busting:) And the fly's have cricket ears. What is THAT all about? ppolish

BA77 Thank you for the information. Dionisio

Dionisio this may help a bit Demise of the Gene - September 19, 2012 Excerpt: Although the gene has conventionally been viewed as the fundamental unit of genomic organization, on the basis of ENCODE data it is now compellingly argued that this unit is not the gene but rather the transcript (Washietl et al. 2007; Djebali et al. 2012a). On this view, genes represent a higher-order framework around which individual transcripts coalesce, creating a poly-functional entity that assumes different forms under different cellular states, guided by differential utilization of regulatory DNA. (What does our genome encode? John A. Stamatoyannopoulos Genome Res. 2012 22: 1602-1611.) http://www.evolutionnews.org/2012/09/demise_of_the_g064371.html Gene activity and transcript patterns visualized for the first time in thousands of single cells - Oct 06, 2013 Excerpt: The method is so efficient that, for the first time, a thousand genes can be studied in parallel in ten thousand single human cells. Applications lie in fields of basic research and medical diagnostics. The new method shows that the activity of genes, and the spatial organization of the resulting transcript molecules, strongly vary between single cells.,,, The analysis of the new data shows that individual cells distinguish themselves in the activity of their genes. While the scientists had been suspecting a high variability in the amount of transcript molecules, they were surprised to discover a strong variability in the spatial organization of transcript molecules within single cells and between multiple single cells. The transcript molecules adapted distinctive patterns.,,, http://phys.org/news/2013-10-gene-transcript-patterns-visualized-thousands.html Here’s That New Paper Showing the Genetic Regulation Hierarchy - Cornelius Hunter - September 2012 Excerpt: a massive study of the interactions between transcription factors and DNA. The study found that the action of transcription factors falls into three distinct, hierarchical, categories. There are interactions that specify the basic cell type (muscle, skin, nerve, and so forth). Then there are interactions that specify the cell’s sub-identity (the particular type of muscle cell, for example). And finally there are interactions that specify the cell’s response to the current environmental challenges. http://darwins-god.blogspot.com/2012/09/heres-that-new-paper-showing-genetic.html bornagain77

Molecular biology: The ends justify the means A genomic analysis of yeast reveals that individual genes produce a rich complexity of RNA molecules with differing start and end sequences. The variation in these transcripts reflects the diversity of gene-regulation mechanisms. http://www.nature.com/nature/journal/v497/n7447/full/nature12098.html

This was published over a year ago - has it been confirmed or disproved since then? Does it relate to the subject of this thread? Dionisio

Yes, I knew what your point was immediately and agree with you. Mung

I'm not sure if you're joking, Mung. But I was going to point out that the "information flow" in the central dogma doesn't refer to what humans know about biology. Making that mistake is about the only way you could imagine this study relates to the central dogma, as far as I can tell. wd400

wd400:

The roll continues. Unless you want to explain what on earth this finding has to do with the central dogma?

Well, you see, we can now annotate genomic information with information from proteomics, and this shows that information transfer isn't strictly one way, from genome to transcriptome to proteome, as maintained by the Central Dogma. It's simple, really. =P I can't believe I have to explain this to you. ;) To me the even bigger News is, this information that now goes the other way along this "two-way road," where does that information come from? Mung

Evidence of altered RNA stirs debate Sceptics question find that upends biology's 'central dogma'. http://www.nature.com/news/2011/110525/full/473432a.html

This was published about 3 years ago - has it been confirmed or disproved since then? Dionisio

Cells may stray from 'central dogma' The ability to edit RNA to produce 'new' protein-coding sequences could be widespread in human cells. http://www.nature.com/news/2011/110519/full/news.2011.304.html

This was published 3 years ago - has this been confirmed or disproved since then? Dionisio

James Shapiro, as much flack as he has caught from orthodox neo-Darwinists (especially Coyne) must be grinning from ear to ear.

Coyne Disses Shapiro, but Shapiro Inspires Koonin -- and Natural Selection Is the Main Issue Paul Nelson August 28, 2012 Excerpt: Coyne ended his post by complaining that Shapiro's dissent from textbook neo-Darwinism "was an embarrassment to me, for Shapiro works at my university and, in my view, his writings impugn our reputation for excellence in evolutionary biology." [Jim Shapiro's] contention that natural selection's importance for evolution has been hugely overstated represents a point of view that has a growing set of adherents. (A few months ago, I was amazed to hear it expressed, in the strongest terms, from another highly eminent microbiologist.) My impression is that evolutionary biology is increasingly separating into two camps, divided over just this question. On the one hand are the population geneticists and evolutionary biologists who continue to believe that selection has a "creative" and crucial role in evolution and, on the other, there is a growing body of scientists (largely those who have come into evolution from molecular biology, developmental biology or developmental genetics, and microbiology) who reject it. http://www.evolutionnews.org/2012/08/coyne_disses_sh063541.html Revisiting the Central Dogma in the 21st Century - James A. Shapiro - 2009 Excerpt (Page 12): Underlying the central dogma and conventional views of genome evolution was the idea that the genome is a stable structure that changes rarely and accidentally by chemical fluctuations (106) or replication errors. This view has had to change with the realization that maintenance of genome stability is an active cellular function and the discovery of numerous dedicated biochemical systems for restructuring DNA molecules.(107–110) Genetic change is almost always the result of cellular action on the genome. These natural processes are analogous to human genetic engineering,,, (Page 14) Genome change arises as a consequence of natural genetic engineering, not from accidents. Replication errors and DNA damage are subject to cell surveillance and correction. When DNA damage correction does produce novel genetic structures, natural genetic engineering functions, such as mutator polymerases and nonhomologous end-joining complexes, are involved. Realizing that DNA change is a biochemical process means that it is subject to regulation like other cellular activities. Thus, we expect to see genome change occurring in response to different stimuli (Table 1) and operating nonrandomly throughout the genome, guided by various types of intermolecular contacts (Table 1 of Ref. 112). http://shapiro.bsd.uchicago.edu/Shapiro2009.AnnNYAcadSciMS.RevisitingCentral%20Dogma.pdf

Also of interest from the preceding paper, on page 22 is a simplified list of the ‘epigentic’ information flow in the cell that directly contradicts what was expected from the central dogma (Genetic Reductionism/modern synthesis model) of neo-Darwinism.

How life changes itself: the Read-Write (RW) genome. - 2013 Excerpt: Research dating back to the 1930s has shown that genetic change is the result of cell-mediated processes, not simply accidents or damage to the DNA. This cell-active view of genome change applies to all scales of DNA sequence variation, from point mutations to large-scale genome rearrangements and whole genome duplications (WGDs). This conceptual change to active cell inscriptions controlling RW genome functions has profound implications for all areas of the life sciences. http://www.ncbi.nlm.nih.gov/pubmed/23876611 The Genome is a Read-Write Memory System - James Shapiro - video https://vimeo.com/74618934

also of note:

“The genome is an ‘organ of the cell’, not its dictator” - Denis Nobel – President of the International Union of Physiological Sciences video debate - Denis Noble and Sydney Brenner will propose and oppose respectively the motion that: “There is no privileged level of causation: an organism is not defined by its genome” http://www.virtual-liver.de/wordpress/en/2012/07/16/the-virtual-liver-network-keynote-debate/

At the 10:30 minute mark of the following video, Dr. Trifonov, a molecular biologist par excellence, states that the concept of the selfish gene 'inflicted an immense damage to biological sciences', for over 30 years:

Second, third, fourth… genetic codes - One spectacular case of code crowding - Edward N. Trifonov - video https://vimeo.com/81930637

bornagain77

The roll continues. Unless you want to explain what on earth this finding has to do with the central dogma? wd400