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Topics - Dave Hawkins

This will be a review of Denis Noble's paper ...
Claude Bernard, the first systems biologist, and the future of physiology

Denis Noble
First published: 18 December 2007Full publication history
DOI: 10.1113/expphysiol.2007.038695  View/save citation
Cited by (CrossRef): 91 articles Check for updates Citation tools
Article has an altmetric score of 19
This article is based on the Paton Lecture delivered with the same title to the Life Sciences 2007 meeting in Glasgow in July 2007.
Corresponding author D. Noble: Department of Physiology, Anatomy and Genetics, Parks Road, Oxford OX1 3PT, UK.

The first systems analysis of the functioning of an organism was Claude Bernard's concept of the constancy of the internal environment (le milieu intérieur), since it implied the existence of control processes to achieve this. He can be regarded, therefore, as the first systems biologist. The new vogue for systems biology today is an important development, since it is time to complement reductionist molecular biology by integrative approaches.
Many other discoveries of this kind (Finar, 1964) led to the idea that life itself could be reduced to chemistry and physics.   This was the challenge that physiologists such as Claude Bernard faced. His answer was precise. Neither vitalism nor chemical reductionism characterized living organisms.


The principles of systems biology
First principle: biological functionality is multilevel I start with this principle because it is obviously true, all the other principles can be shown to follow from it, and it is therefore the basis on which a physiological understanding of the phenomenon of life must be based.
It is hard to think of a more important overall systems property than the one Bernard first identified.  Yet, the language of modern reductionist biology often seems to deny this obvious truth.


Second principle: transmission of information is not one way The central dogma of molecular biology (Crick, 1970) is that information flows from DNA to RNA, from RNA to proteins, which can then form protein networks, and so on up through the biological levels to that of the whole organism. Information does not flow the other way.
Moreover, the DNA code itself is marked by the organism. This is the focus of the rapidly growing field of epigenetics (Qiu, 2006). At least two such mechanisms are now known at the molecular level: methylation of cytosine bases and control by interaction with the tails of histones around which the DNA is wound. Both of these processes modulate gene expression.
There is nothing new in the idea that such feedback control of gene expression must exist. It is, after all, the basis of cell differentiation. All nucleated cells in the body contain exactly the same genome (with the exception of course of the germ cells, with only half the DNA). Yet the expression pattern of a cardiac cell is completely different from, say, a hepatic or bone cell. Moreover, whatever is determining those expression levels is accurately inherited during cell division. This cellular inheritance process is robust; it depends on some form of gene marking. It is this information on relative gene expression levels that is critical in determining each cell type.

By what principle could we possibly say that this is not relevant information? In the processes of differentiation and growth it is just as relevant as the raw DNA sequences. Yet, it is clear that this information does travel 'the other way'. The genes are told by the cells and tissues what to do, how frequently they should be transcribed and when to stop. There is 'downward causation' (Noble, 2006; chapter 4) from those higher levels that determines how the genome is 'played' in each cell (Fig. 2). Moreover, the possible number of combinations that could arise from so many gene components is so large (Feytmans et al. 2005) that there wouldn't be enough material in the whole universe for nature to have tried more than a small fraction of the possible combinations even over the billions of years of evolution (Noble, 2006; chapter 2).


Third principle: DNA is not the sole transmitter of inheritance The defenders of the original version of the central dogma would argue that, while my conclusions regarding the second principle are correct, what happens when information is transmitted to the next generation through the germ-line nevertheless involves wiping the slate clean of epigenetic effects. Methylation of cytosine bases and other forms of genome marking are removed. The genome is reset so that 'Lamarckism' is impossible.

But this is to put the matter the wrong way round. We need to explain why the genome (usually) reverts to an unmarked state. We don't explain that by appealing to the central dogma, for that dogma is simply a restatement of the same idea.


Fourth principle: the theory of biological relativity; there is no privileged level of causality

Fifth principle: gene ontology will fail without higher-level insight

Sixth principle: there is no genetic program

Seventh principle: there are no programs at any other level

Eighth principle: there are no programs in the brain

Ninth principle: the self is not an object

Tenth principle: there are many more to be discovered; a genuine 'theory of biology' does not yet exist. Well, of course, choosing just 10 principles was too limiting. This last one points the way to many others of whose existence we have only vague ideas. We do not yet have a genuine theory of biology. The Theory of Evolution is not a theory in the sense in which I am using the term. It is more an historical account, itself standing in need of explanation. We don't even know yet whether it consists of events that are difficult, if not impossible, to analyse fully from a scientific perspective, or whether it was a process that would have homed in to the organisms we have, regardless of the conditions. My own suspicion is that it is most unlikely that, if we could turn the clock right back and let the process run again, we would end up with anything like the range of species we have today on earth (Gould, 2002).

World J Biol Chem. 2014 Aug 26; 5(3): 275-278.
Published online 2014 Aug 26. doi:  10.4331/wjbc.v5.i3.275
PMCID: PMC4160521
Life is more than a computer running DNA software
František Baluška and Guenther Witzany

Are cellular organisms only robot-like computing machines that function strictly according to their algorithm-based programming? Or, rather, are they coordinated complex entities that share bio-communication properties that may vary according to different context-specific needs? Is DNA the unequivocal syntax for sequences out of which one can construct living cells, viruses and phages for a household appliance? Or is the superficial molecular syntax of DNA solely the result of evolution's long inserts and deletions of an abundance of various genetic parasites that shape host genomes? The most crucial questions are: do DNA sequences contain a hidden deep grammar structure that varies according to the meaning and context of environmental insults; do DNA sequences match with high fidelity environmental circumstances that led to epigenetic markings and memory? If yes, this would then mean that the identical DNA sequence may have various-even contradictory-meanings. In fact, this scenario is emerging as true[4-8].

Interestingly, in complex genomes like humans, the coding genes are about 1.5% of the total genome whereas the abundance of non-coding RNAs are about 98.5%. This means Craig Venter's household appliance box could focus only on the 1.5% coding sequences. The DNA sequences of genomes do not represent 1:1 depictions of unequivocal coding structures such as genes, but in light of the variety of epigenetic markings-with its executives RNA editing and alternative splicing-can store a multitude of further meanings[4-8].

This means epigenetic marking saves energy costs like in human language. A limited repertoire of signs, and a limited number of rules to combine these signs correctly, enables signs using agents to generate an unlimited number of sentences with a superficial grammar in the visible text and an abundance of connotations by marking through gestures and other conscious and unconscious bodily expressions such as the movements of three hundred different eye muscles[9].


Therefore, DNA organized in chromatin is far more complex than the human-made "software system", except that we are confusing the algorithm-based simulation of real-life storage with the real life, the computer machines with the living cells and organisms, and the self-reproducing automatons with the real-life organisms that can replicate since the origins of life[5,9,14].


The genome itself, via natural genome editing[19], generates large amounts of coherent new sequences and inserts these into DNA genomes without damaging essential protein-coding regions. This is not possible for any human-made software.
The Soap Opera / Re: Some heads are gonna roll
MY personal rules?  If I were making the rules at TR, I would not allow threats of physical violence.
Why not? Why is it fine by you in Charlottesville but not on TR? Especially given that threats on TR are not serious while threats made in Charlottesville obviously were?

You really are getting yourself tied in knots here. By banning threats on TR you effectively wish to bans threats that will not be implemented, but earlier you claimed that threats by Nazis should be allowed as long as they were not implemented. These two positions are conflicting.

Then, as I said, the Nazis in Charlottesville are obviously serious about implementing their threats, since they have already done so to some extent, so your position boils down to supporting the rights of Nazis on the basis that they don't implement their threats even when we know they already have, while wanting to ban threats on TR that effectively have zero possibility of implementation, because hey, y'know, being a "non-violent Nazi" who actually is violent in real life is way better than being an internet warrior on TR who is never going to do anything physically violent.

I suppose this is another example of your high speed mind doing its usual headless chicken impression.

  If I were making the rules in Charlottesville, I would do a lot of research first including long discussions with sitting council members to find out why - if they allow Nazis to march and make physical threats and so on - they feel that's ok.  Perhaps they know things I don't know.  After making a careful evaluation, I would then cast my vote.
Oh, sure. Ok, start with research on Nazis. Perhaps they were just misunderstood. After all they did have very shiny boots.

I took it to the Town Hall as you asked me to do.  Are you going to go there and answer me?  Or not?
I'm going to wait and see if anyone else gives a flying fuck.
It would be nice to know if the Administrators of this forum "give a flying fuck" about the rules here.  Namely, answer a simple question - are physical threats allowed or not?  If so, then I'll shut up about that and maybe start spouting my own physical threats.  Hell ... why not if I'm not going to be banned for it?   Also, I want to know if I - Dave Hawkins - am violating any rules.  If so, then I want to correct that.
I don't know if this is the right subforum, but here goes ...

...Admins need to be encouraged to follow the rules and ban Valor at least temporarily.  Threats of physical violence need to be penalized.
But Dave, by your own professed standards, as written in this very thread, you support Valor's right to threaten violence as long as he doesn't actually implement his threats. At the moment, he's just another "non-violent Nazi", like the people you admire in Charlottesville.

Wait ... hold on ... let's be clear.  What are the rules in Charlottesville?  THAT is the question.

Likewise ... what are the rules of THIS forum?  THAT is the question.

You're an admin.  Can you give me a straight answer to the following two questions ...

1) Is it or is it not a forum rule violation to make physical threats to a forum member?
2) Am I - Dave Hawkins - guilty of breaking any forum rules right now?  If so, please tell me which ones so I can correct that
Take it to the fucking Town Hall if you really wanna go there.
Valor is clearly violating all rule of decency and one poster (Heinz Herzhold) has claimed that he is one and the same as "Bart" who was banned.  A private message from Borealis to me last night causes me to think he's right.

Also, Borealis has just been proven guilty of one serious count of SLANDER against a public figure.  And today she slandered ME over an issue involving links.

Borealis needs to clean up her act or else step aside as an Admin and let someone else take over.
Quote from: Valor on Today at 05:52:57 AM

Hey Hawkins, why don't you shut the fuck up you worthless Nazi piece of shit. If I knew where you lived I would come down there and beat the fuck out of your racist ass. Shut the hell up or I will find out.

yeah I am not surprised. you fuckin nazi scum are all the same, you claim to be big tough guys but when somebody stands up to your racist bullshit you start threating jail and cops. fucking coward. go fuck yourself you worthless shithead.
This is something I have wanted to focus on for a long time so here goes ...

"That is because the rest of us think what we do based on evidence."


It's true.  We do.  You don't.  You think you do, but you don't even know what evidence is.  You think that a persuasive hypothesis is evidence that that hypothesis is correct.  You don't test your hypotheses against data.  In other words, you don't look for the evidence that supports a hypothesis.

You basically go around with your eyes shut to anything you don't want to see. 

So let's dig into this a bit shall we?  I think that I base my views on "evidence" ... you think I don't but you think YOU do ... and so on ... so let's find out ...
Ok men ... confession time ...  is there any  man here that has not looked at a Playboy magazine? Or equivalent?
If they are not, then please explain to me at what point they BECOME babies ... when they exit the birth canal? When the cord is cut?  How about preemies? Are THEY fetuses? Not babies?
Testy has a wonderful explanation up his sleeve for how the layers which include the Tonto Group formed.  Bill Hoesch has a neat little article explaining the horizontal extent of these layers here ... ... in which he observes the following ...
Tonto Group equivalents, that are also amazingly similar, are found across much of North America and are reported also across wide portions of Canada, Eastern Greenland, Scotland, and South Australia. Such persistence of strata is enough to baffle creationist and evolutionist alike. Picture a sheet of copy paper 0.1 millimeters thick that measures 1 kilometer by 0.6 kilometer, then stack three on top of one another. You then have a picture of how thin these three layers are across the breadth of North America.

A sufficient process is needed to explain such persistence. The Genesis Flood is sufficient.

Go, Testy, go!

Following is a revised list, based on feedback received from JonF ...

1) The poop in Rampart Cave Unit A is almost entirely Shasta ground sloth poop with very little of any other kind of feces.  That animal is now extinct.
2) Two ways to study the pooping habits of an extinct sloth would be (a) study the poop itself and (b) study the pooping habits of the closest living relative
2b) Wikipedia describes the (modern) "Sloth" ... link here ...
3) If we read the Wiki Sloth article, we find some curious things ... (a) modern sloths only poop about once a week (b) when they poop, they do so in the same spot over and over again (c) they poop out about 1/3 of their body weight each week
4) From the data given in the Long paper, the info in (3) above and applying a scale factor to scale up from "modern sloth" to the size of a Shasta sloth, we could calculate what would be required for one "Shasta sloth sized modern sloth" to deposit Unit A
5) This has been done by myself with the help of osmanthus and the result is that Unit A represents roughly "15 sloth years" of weekly, year round pooping of one adult Shasta sloth ... or "60 sloth years" of weekly, seasonal pooping (3 months of Spring only)
6) Unit A was supposedly deposited over a 2000 year time frame (not 1500, Faid) determined by carbon 14 (p.1844 first sentence of last paragraph in LH column)
7) Carbon 14 dating ignores theories of catastrophic global resurfacing events within the past 10,000 years.
8.) There is a difference in flora found in the upper part of Unit A compared to the lower part with more succulents being in the lower part

I eliminated Point 9 as it was redundant and I modified the others to be more FACTUAL.

Are we in agreement on these points?
Which is closely related to "Death by Booga Booga" ... the prospect of which always frightened me as a kid ...

This is from Wendell Berry ... " The Unsettling of America"
Since Mike is fairly active here these days, I thought I would re-post this diagram from Brown's book and try to get my head around it again.

Quillette: Psychologists Claim Google Viewpoint Diversity Manifesto Is Scientifically Accurate

by CHARLIE NASH7 Aug 2017276

Four scientists have claimed that James Damore's Google manifesto is scientifically accurate, as reported by Quillette.
Responding to the viewpoint diversity manifesto, which called for more ideological diversity in Google's workplace and pointed out not only the biological differences between men and women but also how these can apply to work, the four scientists deemed the ten-page document to be scientifically accurate.

"The author of the Google essay on issues related to diversity gets nearly all of the science and its implications exactly right," declared Rutgers University Professor Lee Jussim. "Its main points are that: 1. Neither the left nor the right gets diversity completely right; 2. The social science evidence on implicit and explicit bias has been wildly oversold and is far weaker than most people seem to realize; 3. Google has, perhaps unintentionally, created an authoritarian atmosphere that has stifled discussion of these issues by stigmatizing anyone who disagrees as a bigot and instituted authoritarian policies of reverse discrimination; 4. The policies and atmosphere systematically ignore biological, cognitive, educational, and social science research on the nature and sources of individual and group differences."
Some smart person here researched the meaning of the name "Wai Wai" ... the name of the people group in N. Brazil where my father was a missionary.  I can't remember what they came up with? 

Anyone remember?

Someone asked me and I can't recall the answer.
Let's start will Bill Mollison's statement ...

Alan: Perhaps because we're so wealthy that we believe we don't have to.

Bill: Well, I don't call that wealth. You want a definition of wealth from Eskimos, the Inuit? Wealth is a deep understanding of the natural world. I think Americans are so poor it's pitiful, because you don't understand the natural world at all.
Found this by referring to the article list of article citing this ...

Natural genetic engineering in evolution. - NCBI
by JA Shapiro - ‎1992 - ‎Cited by 158 - ‎Related articles

Bacterial linguistic communication and social intelligence

Eshel Ben JacobEmail the author Eshel Ben Jacob, Israela Becker, Yoash Shapira, Herbert Levine
Article has an altmetric score of 21
Full Text
Bacteria have developed intricate communication capabilities (e.g. quorum-sensing, chemotactic signaling and plasmid exchange) to cooperatively self-organize into highly structured colonies with elevated environmental adaptability. We propose that bacteria use their intracellular flexibility, involving signal transduction networks and genomic plasticity, to collectively maintain linguistic communication: self and shared interpretations of chemical cues, exchange of chemical messages (semantic) and dialogues (pragmatic). Meaning-based communication permits colonial identity, intentional behavior (e.g. pheromone-based courtship for mating), purposeful alteration of colony structure (e.g. formation of fruiting bodies), decision-making (e.g. to sporulate) and the recognition and identification of other colonies - features we might begin to associate with a bacterial social intelligence. Such a social intelligence, should it exist, would require going beyond communication to encompass unknown additional intracellular processes to generate inheritable colonial memory and commonly shared genomic context.
Absolutely according to Dave Godfrey.  What say you?
Very detailed article explaining some key parts and pieces to the Trump wiretap saga ...
Trump Is Right: Sweden's Embrace of Refugees Isn't Working
The country has accepted 275,000 asylum-seekers, many without passports--leading to riots and crime.

Feb. 22, 2017 6:43 p.m. ET

When President Trump last week raised Sweden's problematic experience with open-door immigration, skeptics were quick to dismiss his claims. Two days later an immigrant suburb of Stockholm was racked by another riot. No one was seriously injured, though the crowd burned cars and hurled stones at police officers.

Mr. Trump did not exaggerate Sweden's current problems. If anything, he understated them. Sweden took in about 275,000 asylum-seekers from 2014-16--more per capita than any other European country. Eighty percent of ...

[EDIT: Sorry fixed the link]
When a man acquires billions of dollars through complex real estate transactions, invests in many countries, goes on to phenomenal success in television and turns his name into a worldwide brand, it is very unlikely that he is mentally unstable.

When the same man obviously enjoys the love and respect of his children and his wife, who seem to rely on him for support and guidance, it is extraordinarily unlikely that he is mentally unstable.

When the same man walks into the political arena and deftly defeats 16 Republican opponents and then the Democratic heir-apparent to a two-term president's administration, the odds of that man being mentally unstable become vanishingly thin.

And when that very same man attracts to his team the kind of intellect and gravitas represented (to name just a few) by Secretary of Housing and Urban Development Dr. Ben Carson, Attorney General Jeff Sessions, Secretary of State Rex Tillerson and Secretary of Defense James Mattis, a retired Marine Corps general and commander of the U.S. Central Command, he cannot be mentally deranged. Period. It is a statistical impossibility.

Those who assert otherwise are political opportunists, or fools, or both (and I am thinking here, in particular, of Sen. Franken).

President Trump is the first human being to win this nation's highest office without having held any other political office or serving as a general. Most political pundits thought his quest was pure folly. Most journalists assessed his chances as zero. So who was laboring under quasi-delusional thinking? Answer: Not Donald J. Trump.

Anecdotally, by the way, I have never had one bad Trump experience. Not one. I own several of his ties -- all of them of the highest quality. I have stayed in his hotels and never had a single complaint (and I am a born complainer). I have eaten in his New York restaurant -- flawless service, excellent food. I own an apartment at Trump Place in Manhattan. Impeccable design, sturdy construction, fabulous amenities. A mentally unstable man would be unlikely to deliver superior products across multiple industries, don't you think?

If you're still worried about the mental stability of the president, note this: The stock market doesn't like instability. Investors, en masse, can take the measure of a man pretty darn well. The stock market has hit record high after record high since Trump's election, and if you think that's an accident, or that investors have all been fooled, it's time to start wondering about your own capacity for rational thought.
There's a video going around Facebook from that Milo guy that says that Luton has been taken over by Muslim extremists.
Happening right now ... go check it out