Here’s the abstract:
To unveil the still-elusive nature of metazoan replication origins, we identified them genome-wide and at unprecedented high-resolution in mouse ES cells. This allowed initiation sites (IS) and initiation zones (IZ) to be differentiated. We then characterized their genetic signatures and organization and integrated these data with 43 chromatin marks and factors. Our results reveal that replication origins can be grouped into three main classes with distinct organization, chromatin environment, and sequence motifs. Class 1 contains relatively isolated, low-efficiency origins that are poor in epigenetic marks and are enriched in an asymmetric AC repeat at the initiation site. Late origins are mainly found in this class. Class 2 origins are particularly rich in enhancer elements. Class 3 origins are the most efficient and are associated with open chromatin and polycomb protein-enriched regions. The presence of Origin G-rich Repeated elements (OGRE) potentially forming G-quadruplexes (G4) was confirmed at most origins. These coincide with nucleosome-depleted regions located upstream of the initiation sites, which are associated with a labile nucleosome containing H3K64ac. These data demonstrate that specific chromatin landscapes and combinations of specific signatures regulate origin localization. They explain the frequently observed links between DNA replication and transcription. They also emphasize the plasticity of metazoan replication origins and suggest that in multicellular eukaryotes, the combination of distinct genetic features and chromatin configurations act in synergy to define and adapt the origin profile. (paywall) – Christelle Cayrou, Benoit Ballester, Isabelle Peiffer, Romain Fenouil, Philippe Coulombe, Jean-Christophe Andrau, Jacques van Helden & Marcel Méchali.Genome Research, 11 November 2015.
These researchers’ findings make the genome sound like a committee, but without the usual duds, drones, and discards from more productive work groups that most human committees feature.
Thoughts?
News:
There is this, too:
“High-resolution profiling of Drosophila replication start sites reveals a DNA shape and chromatin signature of metazoan origins.”
http://ac.els-cdn.com/S2211124.....5cd1d2d7ec
Abstract:
And this:
“DNA replication origins.”
http://www.ncbi.nlm.nih.gov/pm.....MC3783049/
Abstract:
And this:
“The Dynamics of Eukaryotic Replication Initiation: Origin Specificity, Licensing, and Firing at the SingleMolecule Level”
http://ac.els-cdn.com/S1097276.....cb8d9f5b06
Abstract:
Fascinating subject. As Dionisus would say: “Complex complexity”. Indeed!
Two points are probably worth of special consideration:
a) The epigenetic control of replication origins. As usual, complex and flexible.
b) the rather amazing connection between DNA replication organization and transcription organization.
I don’t know what to say, but if I were a sincere neo darwinist, the emerging landscape of epigenetic control would probably encourage me to consider (intellectual) suicide.
We have been saying many times, during the last few years, that the emerging complexity revealed by daily biological research is probably the strongest, ongoing argument for design.
That is absolutely true. But I must say that the emerging functional complexity of the epigenetic landscape is really beyond all my most optimistic expectations!
News:
Mcm2, one of the key factors in replication initiation, is a very conserved molecule in eukaryotes:
Human – saccharomices cerevisiae blast:
Score: 778 bits(2010)
Expect: 0.0
Identities: 416/864(48%)
Positives: 557/864(64%)
Gaps: 76/864(8%)
Length of human protein: 904 AAs.
Even more so in vertebrates:
Human – Callorhinchus milii (shark) blast:
Score: 1587 bits(4108
Expect: 0.0
Identities: 762/906(84%)
Positives: 834/906(92%)
Gaps: 22/906(2%)
Length of human protein: 904 AAs.
From Wikipedia:
What a delightful present for the weekend.
News posting such a highly interesting and important topic and then to make it much better, gpuccio starts the follow-up discussion with his always very insightful comments, loaded with juicy information.
Thank you News and gpuccio!
Complex complexity.
Work in progress … stay tuned.
Complex complexity.
Complex complexity.
Work in progress… stay tuned.
Complex complexity.
Work in progress… stay tuned.
We’ve known about origins of replication for almost 50 years. I worked on them a little bit when I was a graduate student in 1968.
They are included in the functional part of the genome [What’s in Your Genome?].
In fact, they are some of the well-known functional noncoding DNA sequences that I use to refute claims about noncoding DNA equaling junk DNA. Those claims by ID proponents (and some scientists) are false. There was never a time when knowledgeable scientists thought that all noncoding DNA was junk.
Note: UD is inserting stuff into my comment that sometimes screws up the formatting. It is adding ‘rel=”nofollow”‘ to URLS. It’s not my fault.
Prof Moran
I take then that Richard Dawkins is not a knowledgeable scientist but quite possibly a nimcompoop?
Andre asks,
I take then that Richard Dawkins is not a knowledgeable scientist but quite possibly a nimcompoop?
He’s not a nimcompoop.
He and I disagree on a number of things. We’ve been arguing about them for almost twenty years. He continues to comment on Sandwalk from time to time. I’ve been to his house in Oxford to discuss our differences over molecular evolution.
We respect each other’s position even though we each think the other person is wrong.
Richard Dawkins Talks About the Human Genome
Richard Dawkins’ View of Random Genetic Drift
Granted then not a nimcompoop but not knowledgeable either.
I’ve been to his house in Oxford to discuss our differences over molecular evolution.
Did that come in a mug or a bottle?
Additional related papers referenced @1153-1160 here:
http://www.uncommondescent.com.....ent-587959
Larry Moran @8
Since then, some outstanding questions have been answered, but new important questions have been raised.
That’s why we look forward, with growing anticipation, to reading future research papers that might shed more light on the elaborate cellular and molecular information-processing choreographies orchestrated within the biological systems.
This is a fascinating time to look at the very interesting data coming out of biological research, which is increasingly revealing a marvelous complexity that is turning more complex with every discovery.
Just look at gpuccio, an experienced medical doctor, who reacts with such a contagious enthusiasm at the latest publications of new biological discoveries. Here’s a recent example: http://www.uncommondescent.com.....ent-588110
Facing so many interesting research papers we feel like children in a gigantic toy store.
As researchers dig deeper into more accurate levels of details, they discover more purpose-driven specified functional prescriptive information being transmitted and interpreted within the biological systems.
Complex complexity. Indeed!
The more we know, the more we have to learn.
Unending Revelation of the Ultimate Reality.
Professor Moran writes:
Well, if we’re talking about all noncoding DNA, then Professor Moran is of course correct. But if we’re talking about most DNA, that’s another story entirely:
While Professor Moran is here, I have a few questions for him. I’m still making up my mind about what proportion of the human genome is functional. Recently, I watched Professor P.Z. Myers’ 2011 talk on junk DNA and I thought he’d made a pretty convincing case (but see here fro another perspective), especially regarding LINEs and SINEs. But then I had a look at Dr. Richard Sternberg’s posts on LINEs and SINEs (see here, here and here), and I have to say I thought Dr. Sternberg made a good case for these segments being the product of design. Surprisingly, despite the fact that his posts were written five years ago, I haven’t seen a refutation from the “unguided evolution” camp, yet. Do you have any comments, Professor Moran?
I’ve had another thought about Carl Zimmer’s article. Zimmer writes:
Professor Moran, are you aware of any evidence that the genomes of organisms living 10 million, 100 million or 500 million years ago were smaller on average than they were today?
Finally, here’s a thought for ID theorists to ponder. Zimmer’s article argues that if every piece of the genome were essential, then the human species would become extinct in less than a century. On that logic, there must be some critical percentage P of junk DNA in the human genome that would allow the human species to continue over very long periods of time (say, a million years). What I’m suggesting is that junk DNA could itself be a design feature, and that the percentage of junk DNA should be no higher than it needs to be, to ensure the long-term survival of the species.
Thoughts?
VJ:
Just a few thoughts:
a) Transposons are certainly a powerful tool for the remolding of the genomes in the course of natural history. Whether such remolding is a random functionless process, or a guided one which designs function, or just the occasional object of random “exaptation” leading to function by mere luck, remains to be decided, and could be one of the important fileds of confrontation between ID and neo darwinism (in any of its forms).
b) Saying that “every piece of the genome is essential” is not the same as saying that every piece, or most, of the genome is functional. Function is not the same thing as essentiality. We learn from design in general, and from biology in particular, that many functions can be redundant, and that a good design is often associated to “escape routes”, to alternative ways of doing the same essential thing. Epigenetics is a wonderful example of many different levels interacting in flexible ways to realize highly efficient control. Therefore, a lot of the genome could be functional without being essential, and so the human species, as well as other species, can probably avoid becoming extinct in less than a century.
Vincent Torley says,
Thanks. Let’s put a stop to this stupid myth about scientists thinking that since only 2% of our genome encodes protein therefore all the noncoding DNA (98%) is junk. It started out as a misconception (perhaps) but now it’s a lie to repeat it.
What you have to keep in mind is that the vast majority of SINES and LINES contain mutations that make them unable to transpose. In most cases, the signals consist of little more than bits and pieces of sequences that use to be intact SINCE and LINES. The total number of functional transposons in the genome accounts for less than 1%.
About 50% of the genome consists of defective bits of transposons. That doesn’t look like design to me. It looks like pseudogenes.
I count the functional transposons as part of the functional fraction of the genome.
Furthermore, it doesn’t make sense to postulate that all the defective transposon fragments have secondarily acquired a function. There’s suggestive evidence that a few of them might have a new function but even in order to arrive at a “few” you have to add together results from a dozen different species.
Also, when you are thinking about this issue, remember that every newborn baby has about 100 new mutations. If most of our genome were functional then a huge number of these mutations are going to be detrimental and our species could not survive. It follows that most mutations have to be neutral which means that most of our genome has to nonfunctional junk DNA. This is the genetic load argument for junk DNA first advanced in the late 1960s.
We talked about this when Carl was in Toronto last December preparing this article.
Junk DNA comments in the New York Times Magazine
I don’t agree with Carl. I don’t think there’s any evidence that the immediate ancestors of humans had smaller genomes.
However, it seems reasonable that once you get back 500 million years or so it’s very likely that our ancestors had smaller genomes.
This doesn’t make sense. Why couldn’t our genome be one-tenth the size it is now in which case there would only be 10 mutations per generation? (The number of mutations per generation depends on the amount of DNA that’s being replicated.)
This is what we see in pufferfish where a much smaller genome seems to work just fine.
This is where the Onion Test becomes useful. Does your speculation pass the Onion Test?
gpuccio @16
Regarding your second item (b) in your commentary, would the following example qualify as a case of a designed object component or feature that is functional but not essential?
The small TV screens that are attached to the back of the seats in the economy class of some airplanes are not essential, but definitely have a function. My wife sometimes watches films during our long flights. However, I rarely look at those screens, because I usually just read offline a few PDF documents I download before the flight. Another thing I consider very handy is the power outlet located right between our two seats, which allows me to charge my tablet during long flights. Though functional, that power outlet is not essential.
If any of those two things (or both) were broken or removed, we still could get to our destination, assuming all the essential parts were in place and well.
BTW, not sure if this is ‘off topic’ for this current thread, but wanted to let you know that for some reason your name came to my mind when I saw this:
http://www.sciencedirect.com/s.....20/supp/PA
@10
Larry Moran “He and I disagree on a number of things. We’ve been arguing about them for almost twenty years. He continues to comment on Sandwalk from time to time. I’ve been to his house in Oxford to discuss our differences over molecular evolution. ”
Now I heard a rumor that I would like Professor Moran to confirm or deny if possible.
I heard this rumor that when you went to Dawkins house, that you asked him where your cup of tea was and that Dawkins said that he was waiting for the tea to be made by chance for you.
I heard that you got your own back though and when it came to the roast dinner then you started throwing the roast potatoes from your plate and when Dawkins said to you, what the hell are you doing Larry?
Then you said, Richard, I am just testing the hypothesis that selecting something for elimination from my plate is going to create something that never was on my plate.
Did this happen Professor?
Dionisio says,
I understand the feeling. I feel the same way when I read papers about astrophysics. Then my daughter (Ph.D. in astrophysics) explains to me that they already new that; it’s wrong; or it’s just an incremental addition to what they already know.
Those are pretty much my reactions when I read about “exciting” new discoveries in biochemistry, molecular biology, and evolution. It a rare day when I read something new that has to go into my textbook.
Dionisio, I’m certain that you are an expert on something. When you read popular press reports about new and exciting discoveries in your field do you feel like a child in a candy store or do you recognize that the popular press exaggerates a little bit?
That’s an incorrect statement, verging on a lie.
“Researchers” are NOT discovering “purpose-driven specified functional prescriptive information.” Just the opposite. Researchers in general are still convinced that there’s no evidence of purpose in biochemistry and molecular biology.
What you may be seeing is propaganda from Intelligent Design Creationists who are interpreting the data according to their preconceptions of what it should be demonstrating.
Lawyer Barry Arrington will explain to you why their logic is faulty and their assumptions are incorrect.
BTW, I can see now that you probably weren’t telling the truth when you implied earlier that you had an open mind and just wanted to learn about developmental biology. Here’s what you said a few days ago …
Here’s what you said today.
Your mind is already made up. Sharing “vast knowledge” with you is just going to be a waste of time.
Dionisio asks,
This blog would be an even better example. 🙂
Larry Moran is old-school and still believes that organisms are little machines that are controlled by DNA and the environment.
He tries to keep up and claims to have read ‘Darwin’s Doubt’, but he obviously skipped over the part on epigenetics. The days that DNA ran the show are long gone Larry ….
Larry Moran @20
Is yours a scientific statement?
Larry Moran @20
Professor Moran,
Apparently you started our chatting in this UD blog last October, didn’t you?
Can you explain what motivated you to write to me first?
Here’s a quick hint:
http://www.uncommondescent.com.....ent-587914
BTW, I assume you don’t have to consult your academic colleagues in order to prepare for answering the above question, do you? 🙂
Dionisio @18:
Yes, your example is fine. I would add redundancy to the model: maybe your wife looks at movies in the small video, and maybe you can look at movies on your laptop. You both attain the same result, in different ways.
Larry Moran adds that “This blog would be an even better example”. I can agree. Knowledge and intellectual confrontation are probably not essential. From some point of view. More essential from others.
What is certainly “functional”, but not essential, and probably not even desirable, is the self-assurance of those who, considering themselves experts (and being indeed experts), think that they can impose their views by authority and maybe arrogance, instead than by honest and patient and respectful intellectual confrontation, however non essential it may be.
Larry Moran seems to be in denial about the challenge for neo-darwinian (and neutral theory) evolution posed by epigenetics. On the Sandwalk blog, march 2014, Larry writes:
That would be the day!
It’s pretty obvious why Larry is in denial mode: epigenetics spells disaster for his position.
gpuccio @25
Eccellente!!!
Mile grazie mio caro amico Dottore!
Larry Moran @20
Well, sorry to disappoint you, but I’m not an expert on anything, not even on my own ignorance.
BTW, I suffer an incurable natural human malady that makes me resistant to admit my ignorance.
Larry Moran @20
Huh?!
🙂
gpuccio @25
Yes, agree. Good catch! Thank you for adding it.
I missed that important part, which is seen in some well designed complex models, like in large passenger airplanes or computer servers for banking systems.
BTW, sometimes I’ve noticed in some biology research papers, that their experiments intentionally altered something within the observed system, apparently expecting to see a particular behavior change, but were surprised to discover that the affected system still managed to ‘survive’ or get away with the introduced ‘alteration’. Then sometimes the given conclusion referred to some kind of unexpected redundancy. Did I understand that correctly?
Hi Professor Moran,
Thank you for your response. You wrote:
I’d like to ask you a couple of questions.
1. Do scientists have any idea yet why pufferfish have such small genomes, or why onions have such large ones? It strikes me that until we can answer these questions and make quantitative predictions about the size of an organism’s junk DNA, we can’t really be said to have a scientific theory of junk DNA.
2. I understand that fish in a closely related family have genomes that are twice the size of pufferfish. What happens when scientists remove the excess DNA from the genomes of some of these fish and breed them for a few generations? Has this experiment been attempted, and if so, were any deleterious effects observed in the population with pruned DNA? Just curious.
3. I understand that similar experiments were performed in mice a few years ago. Casey Luskin has a report on it here: http://www.evolutionnews.org/2.....62001.html
Are there any comments you’d like to make on his piece?
Thank you.
Vincent Torley asks,
No, we don’t know why pufferfish have small genomes and we don’t know why two closely related species of onion can have very different genome sizes.
We don’t have (or want) a scientific theory of junk DNA in the sense you imagine. We’re talking about the history of life here and these are unique events.
The very best we can do is to make sure that evolutionary theory isn’t violated or refuted by the existence of species with lots of junk DNA in their genome. In other words, evolutionary theory has to be compatible with what we observe.
The older version of evolutionary theory (Darwinism) was NOT compatible but the modern version that includes Neutral Theory, random genetic drift, and advanced population genetics IS compatible.
The modern version of evolutionary theory would strongly suggest that species with large population sizes and rapid reproduction rates would not have much junk DNA in their genomes. I would also indicate that species with small populations and slow reproduction rates would probably have a junky genome. These are probabilities. That’s how biology works. Within the range of probably outcomes there are always going to be species in the tails of the probability distribution.
You can’t predict which particular species will have a genome size of “x.”
Think of it this way. The laws and theories of physics are very robust and well-confirmed. Yet they cannot predict how many planets we will find around a given main sequence star. Surely you don’t think that’s a flaw in the theories, do you?
Or try this. Our understanding of what causes cancer is getting quite sophisticated. But we’ll never be able to predict whether a given person will get bladder cancer or not. The best we can do is assign probabilities. We won’t throw out our understanding of cancer if the person dies of a heart attack when they are 110 years old or if they die of leukemia when they are a child.
You are asking for the impossible when you demand a theory that makes “quantitative predictions about the size of an organism’s junk DNA.” I’m surprised you don’t know this since you are an intelligent design proponent.
Or am I missing something? Does ID make such quantitative predictions about junk DNA?
No, nobody has done those experiments and nobody is ever going to do them. The experiment is too difficult and expensive and there are better ways to determine if the excess DNA is junk or not.
Two large sections of the mouse genome were deleted in a small-scale attempt to see if any of the putative genes in those regions really were genes. The mice seemed to survive very well suggesting strongly that there not dozens of functional genes in those regions as some people were predicting.
Larry Moran, “Two large sections of the mouse genome were deleted…” Isn’t this the study where some of the deleted DNA is highly conserved, yet they found no obvious deleterious effects to the mice. What would cause this DNA to be conserved? Is there some tool that unusually conserves DNA other than natural selection?
Box says,
Really? Let’s take methylation of DNA as one of the classic example of epigenetics. We’ve known about that for 40 years and I’ve been teaching it for almost as long.
We know the enzymes and we know how they work. We know how the epigenetic marks are inherited.
Epigenetics
Restriction, Modification, and Epigenetics
Not it’s entirely possible that I could be wrong about epigenetics and it really does present a challenge for evolutionary theory. Maybe I just missed it sometime over the past four decades.
However, quoting Stephen Meyer as your authority on this subject seems to violate some of the principles you adhere to; namely, demanding that your “expert” really is an expert.
gpuccio RE: posts #18, #25, #30
If one or both of the mentioned nonessential functional parts, subsystems or mechanisms (small TV screens and power outlet) get removed, would the airplane still be able to perform its main function – i.e. fly and transport people from a location to another?
Are there equivalent situations in biology research?
Professor Moran,
Would you mind answering the questions @23 & @24?
Thank you.
Here’s the link to post 23:
http://www.uncommondescent.com.....ent-588266
Professor Moran,
Would you mind answering the questions @23 & @24?
Yes.
I’m only going to engage people who ask honest questions and genuinely want to learn something or have a serious discussion.
I’ll ignore everyone else. That includes you.
Still not sure about Box.
Larry Moran:
What does that mean, Larry? Does it mean we knew it had an origin because we don’t know how it originated, even to this very day.
Also can you link to this alleged evolutionary theory so we can all see what it actually says so we can all see what actually challenges it?
One more thing- you still have no idea what determines an organism’s final form. Your reference to Venter proves that you don’t have a clue.
Cain:
Yeah. Let’s see this theory, especially the all-important chapter on how to conduct experiments to falsify it.
Never mind. I was just joking. I know I’m dealing with pseudoscientists, charlatans and impostors.
Virgil Cain @39
Perhaps you misunderstood the term ‘origins’ in Professor Moran’s comments?
I think he’s referring to DNA replication origins, not to OOL. But I could be wrong too.
You may want to read the first few lines @4 in this thread to see what the word ‘origins’ mean in that case.
Mapou @40
You may want to look at comment @41.
Larry Moran @38
Are you saying that the questions @23 & @24 are not honest?
Why? Can you explain your opinion?
Are you quitting because you’ve found my simple questions difficult for you to handle? Why? They couldn’t be easier.
Is this how you treat your students too?
Is this how you relate to other people?
Can you do better than this?
BTW, regarding honesty and seriousness, please take a look at my comments @41 & @42.
Sorry to see you giving up this early in our discussion.
Please, reconsider your decision. Take a break, rest and then think about it again.
More fundamentally it poses a challenge for any naturalistic bottom-up explanation of an organism. In order to provide such a bottom-up explanation naturalism requires a ‘master-controller’ at the level of the parts — and the sole candidate seems to be DNA.
A ‘master-controller’ is by definition a “self-mover”, that is it controls itself. This is a highly debated concept in philosophy — with strong relations to the concept of freedom, responsibility, ‘causa sui’ and God. Yet the very concept of ‘self-control’ seems to lie at the heart of the naturalistic concept of an organism; projected in DNA.
The naturalistic idea is that DNA controls the various factors that control DNA, so that, in effect, DNA controls itself. I have asked Larry Moran how that concept makes sense.
Larry Moran doesn’t see any problem. The DNA-molecule directs itself “easy”.
A tightly regulated program is being executed like clockwork. This is the naturalistic concept of an organism.
Apart from epigenetics there are more basic challenges for this view, for instance:
The multi-cellular organism
//In post #22 I quote S.Meyer who points at “membrane targets” during the embryogenesis of fruitflies*, which are arguably independent from DNA and therefore contradict Moran’s statements.//
Returning to my more general note: especially during the main period of an organism’s development there simply has to be a higher level of an organization that directs DNA in the individual cells. The concept of millions of ‘master-controllers’ that operate independently from each other is simply incoherent.
There has to be a center of control.
Naturalism cannot ground such a single center of control and therefor it fails to explain an organism. This is my fundamental insight.
Note that it is not enough for DNA in individual cells to “communicate” with each other. The problem that needs to be solved has organizational and authoritative aspects.
//
[* Frohnhöfer and Nüsslein-Volhard, “Organization of Anterior Pattern in the Drosophila Embryo by the Maternal Gene Bicoid”; Lehmann and Nüsslein-Volhard, “The Maternal Gene Nanos Has a Central Role in Posterior Pattern Formation of the Drosophila Embryo.”
&
Roth and Lynch, “Symmetry Breaking During Drosophila Oogenesis.”]
Box: There has to be a center of control.
That’s your presupposition, not an argument.
The argument I provided is that “the concept of millions of ‘master-controllers’ that operate independently from each other is simply incoherent.”
I can easily provide an example:
When we visit a car assembly plant and see how all sorts of disjoint parts, robots and craftsmen work in concert and reach a common goal, then we immediately understand that there has to be a center of control.
The alternative “all agents at the plant work completely independent from each other — each of them decides on its own what to do — but somehow things fall together perfectly every time” fails to make sense.
Professor Moran,
Thank you for your comments. I understand your point that it is unreasonable to ask for an explanation of a particular event when that event is governed by a probabilistic law. One does not ask why a radioactive decay event occurred here and now, for instance. Nevertheless, I would argue highly anomalous events require an explanation of some sort (e.g an exceptionally large or small genome size), as well as patterns which appear in certain classes of events (e.g. salamanders in general have very large genomes).
I found out, by looking up the genome sizes of various fish species, that the genome of the pufferfish, while small, is not exceptionally so. I’ve also found out that organisms with small genomes tend to lose nongenic DNA very quickly, while organisms with large genomes tend to lose this kind of DNA very slowly.
I also checked out what you wrote about effective population sizes, and it turns out that pufferfish have an effective population size of 10^5, which is quite large for a vertebrate (cf. 10^4 in humans).
I’m afraid haven’t been so lucky with onions: I haven’t found any evidence of small populations and slow reproduction rates, which could explain their large genomes. Polyploidy doesn’t apply to them either, according to T. Ryan Gregory.
Thanks for the information on DNA deletion experiments in mice.
@43″Are you quitting because you’ve found my simple questions difficult for you to handle? Why? They couldn’t be easier.”
It could be because you exposed him, When I exposed Moran on his Blog then he started deleting my responses to him.
It also could be because he does not know. Larry Moran does not even know whether the evolution that he believes in, occurs according to need or irregardless of need.
He is talking respectfully to some people here but then he will use the term IDiots on his blog.
He is two faced and infantile for an academic and does not deserve any respect.
I was respectful to him but he did not want to reciprocate, You have been respectful and see how he has ended up responding to you.
Box: The alternative “all agents at the plant work completely independent from each other — each of them decides on its own what to do — but somehow things fall together perfectly every time” fails to make sense.
That can occur when everyone’s success depends on the success of the whole, even though there is no master control. It can happen even when no one is aware of the overall global structure, such as the “invisible hand” of the market.
Zach,
are you arguing that a multi-cellular organism can be “explained” by millions of cells who operate independently from each other?
Let’s be clear on this. Is that what you are you saying?
Jack Jones @48
Yes, I see what you mean.
Perhaps the professor is not aware of the poor impression his attitude and behavior have left in a public forum like this, where so many anonymous lurkers read the posted comments and draw their own conclusions accordingly.
I think my questions were simple, straightforward, easy to respond honestly. However, some of them reveal motives.
Sometimes people don’t like to expose their motives.
Given his alleged academic credentials and scientific experience, I thought the professor would provide links to interesting research papers and/or bring to our discussion very knowledgeable specialists in the discussed topics.
Maybe still it’s possible the professor will reconsider his decision and come back to discuss seriously?
Jack Jones
Regarding your comment No. 48, may I disagree?
Professor Moran has been respectful but I don’t think Dionisio has been respectful. Clearly his comments are intended to discredit the professor, maybe because he disagrees with the professor’s position. That’s unfair, isn’t it?
Did you read Dionisio’s strange questions? They are not clear, very confusing. Not the standard questions we should expect in a forum like this. Obviously made with the intention to bother and mortify.
Why do they allow that kind of behaviour in this site?
Maybe because Dionisio is one of the ID proponents he can get away with it?
Is that why he is allowed to mistreat the professor publicly?
Dionisio
Regarding your comment No. 51
Shame on you!
Your comment is not true.
You should learn to be more respectful of others.
DTZ @ 53
Please, calm down.
Are you sure you know well what you’re commenting on?
I respect your opinion, but that’s just an opinion.
What you wrote @52 is also off target.
// Rephrasing my argument against naturalistic gene-centric biology, which I argued in #44 and #46:
– – –
(1) Multicellular organisms, consisting of millions of individual DNA strings which work as a team, exist.
(2) This teamwork of millions of individual DNA strings in a multicellular organism is inconceivable absent a level of control over and above the individual DNA strings.
(3) Naturalistic gene-centric biology denies the existence of a level of control over and above the individual DNA string.
Conclusion: naturalistic gene-centric biology cannot explain multicellular organisms, as defined in (1).
Box: are you arguing that a multi-cellular organism can be “explained” by millions of cells who operate independently from each other?
You are claiming that global structures can’t occur due to local non-guided interactions. That is not correct. A flock forms due to the interaction between neighboring birds without regard to any global pattern.
During embryogenesis, each cell gives and receives messages from neighboring cells, and keeps a record of its own proliferation. Scientists have manipulated this process in order to understand its workings. The process is very similar for most of metazoa.
https://en.wikipedia.org/wiki/Cell_fate_determination
Box: This teamwork of millions of individual DNA strings in a multicellular organism is inconceivable absent a level of control over and above the individual DNA strings.
https://www.youtube.com/watch?v=Z3sLhnDJJn0
My claim is not simply that “global structures can’t occur due to local non-guided interactions”. The sun has a global structure which arguably arises due to local non-guided interactions.
My claim is that the astounding level of cooperation between millions of individual DNA strings that we see in a multicellular organism, which is beyond any comparison — the amazing coordination of a flock of birds included —, must have an explanation that includes a level of control over and above the millions of individual DNA strings.
You link to a Wiki page, but it doesn’t offer a coherent concept of a bottom-up explanation. It points out that particular proteins and mRNAs are involved in embryogenesis but that doesn’t begin to explain how they can conceivably direct a process which inevitably requires a higher level of control and overview.
In the article is a link to cell-cell communication in plants embryogenesis, but such communications are “horizontal” and therefore don’t explain what needs to be explained. Again, what is needed for things to make sense are coherent clear “indisputable” instructions for millions of individual DNA strings from a higher level.
Box: My claim is not simply that “global structures can’t occur due to local non-guided interactions”. The sun has a global structure which arguably arises due to local non-guided interactions.
You said, “The concept of millions of ‘master-controllers’ that operate independently from each other is simply incoherent.” The Sun is made up of millions of individual particles operating independently from each other that control the global structure.
Box: My claim is that the astounding level of cooperation between millions of individual DNA strings that we see in a multicellular organism, which is beyond any comparison — the amazing coordination of a flock of birds included —, must have an explanation that includes a level of control over and above the millions of individual DNA strings.
A flock of birds, a school of fish, a swarm of insects, all form from a few simple rules. Basically, individuals just keep a certain distance between themselves and their neighbors. It’s an emergent behavior that does not require any central coordination. It’s simple to simulate.
By the way, the use of adjectives, such as ‘astonishing’, doesn’t imply incoherence.
The rules of design.
Simple indeed. Too simple! You point out that all the birds do the same thing: they “just keep a certain distance between themselves and their neighbors.” But that is exactly the reason why your comparison isn’t apt. You might have had a point if a flock of birds started to morph into different parts and self-organized into an airplane.
Although such a phenomenon would immediately raise questions: how do the birds know which parts they should form and what directs the different parts to their unique locations?
In other words, what is the higher level of control?
Box: Simple indeed.
You claimed that “the amazing coordination of a flock of birds” must have a level of control over and above the actions of the individual birds. However, we know that global patterns can emerge from very simple rules, including flock behavior.
Can you point out where I made this claim? To my knowledge I did not make that claim.
Zachriel: You are claiming that global structures can’t occur due to local non-guided interactions. That is not correct. A flock forms due to the interaction between neighboring birds without regard to any global pattern.
Box: My claim is that the astounding level of cooperation between millions of individual DNA strings that we see in a multicellular organism, which is beyond any comparison — the amazing coordination of a flock of birds included —, must have an explanation that includes a level of control over and above the millions of individual DNA strings.
Please note that you were responding to the example we provided concerning flocking behavior.
Zach #63:
You quote me saying:
Here I meant to say that the “astounding level of cooperation between millions of individual DNA strings that we see in a multicellular organism” cannot be compared with anything — “beyond any comparison”. “The amazing coordination of a flock of birds included“ means that a flock of birds also fails as an apt comparison.
Well, then we’re just left with your bald claim.
If I’m right and there is a higher level of control — and indeed there has to be — then this level ceases its activity at the moment of death.
Box: If I’m right and there is a higher level of control
Conditional.
Box: — and indeed there has to be —
If there has to be, then it follows deductively, but you’ve provided nothing more than ‘It’s astonishing, how could it not!’
Box: then this level ceases its activity at the moment of death.
Tautology. Death is defined as the cessation of living activity.
I’m afraid the bald claim stems from you, or rather naturalism. And I would like to go even further, and state that the naturalistic claim that the astounding coordinated effort of millions of individual blind DNA strings that bring about a multicellular organism, which makes a performance of St. Matthew Passion by the Berlin Philharmonic Orchestra pale in comparison, does NOT need a level of coordination over and beyond the individual DNA strings is beyond bald; it goes against basic reason.
Box: I’m afraid the bald claim stems from you, or rather naturalism.
To which you reply with another bald claim.
Box: it goes against basic reason.
Rather, it goes against your incredulity — not the same thing at all.