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Messages - JonF

1
I refuse to entertain this perennial bullshit nonsense about copying errors in DNA not being mistakes. Utterly ridiculous and I refuse to waste my time.
How does a chemical reaction make a mistake?
By not copying the correct thing from the template. I don't know ... go ask a biochemist. It's them saying it, not me.

We know you don't know.  That's exactly the point we are making. You are simply bullshitting.

You can't even grasp the difference between somatic and germline mutations, or understand that bacteria reproduce by copying themselves, while multicellular sexually reproducing organisms like people and sheep (which was where this discussion started, remember) don't.


Look you idiot I know enough to be able to read what a biochemist says about copying errors in DNA.
No, Davie-doodles, you don't know enough. As demonstrated by your misunderstanding of what you "read".
2
Lots of chaff and flares here ...

To clear things up ... let's state things simply ...

1) ST started this whole thing by saying that "biological software" looks like it was poorly designed ... as if by a trial and error process
2) I countered by asking "how can you be qualified to judge it's quality when we are only familiar with 1.5% of it - the coding regions?"
How are you qualified to discuss the topic?
3
One thing you seem to miss is - as Ayala observed in that quote that I wheel out every so often - most of the variation we see in organisms already exists within the respective genomes.  What does NOT exist previously within genomes is random stuff - mistakes - which the cell is designed to rigorously try to prevent.  And it does a damn good job, but not perfect as we have often discussed.  So mistakes happen and so we do get new variants.  And there are almost zero examples out of trillions of any of these random variants that can be in any way spun as being "beneficial" to the organism or the population.
Sort of.  But the number of beneficial mutations is not zero, as you just acknowledged.

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The number may actually be zero now as we have learned more (for example, antibiotic resistance in bacteria used to be the "textbook example" of random mutations being beneficial but that crashed and burned).
We've been over this before.  Antibiotic resistance in bacteria is one of many examples of beneficial ransom mutations.
4

Quote
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].

EPIGENETICS: HIDDEN DEEP GRAMMAR
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.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4160521/
The best designs are simple.
Complexity is a sign of bad design.
Simplicity is hard. Complexity is something that happens if you don't prevent it.

Also, this
Quote
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.
is nonsense. Software used to work like that, it turned out be be a spectacularly bad idea. We stopped doing it that way.
Hahahahahaha

Yeah ... organisms don't operate very well ... if God would just update the software ...

Lolololol
That's all you got out of that?

Moran.
5
Do you think the software that you write is as sophisticated as the software employed in the biological world? I happen to think that it's nowhere close. And Bill Gates is actually on record agreeing with me. Which begs the question... What makes you feel qualified to judge the quality of biological software?
I'm not talking about the function and what is aparent on the outside. I'm talking about internal structure, the way it is put together, the design or lack of it.
I'm thinking of things like the laryngeal nerve in giraffes, whale pelvises, marsupial birth and development of kidneys in mammals. These things have familiar patterns commonly found in badly designed sofware.
Woodpecker's tongue.
6
How appropriate that Fred wrote "asses."
That is a good description of your evaluation method.
7
It's easy to only have maintenance-free things. Just get rid of anything you have that requires maintenance!
Yup ... that's the idea.
And replace it with a new one.

So sustainable. So efficient.
It's actually quite.  On both counts.  I'm surprised you've never heard of artificial selection.  People have doing it for thousands of years.
That's not artificial selection, you moron. What the guy you got your sheep from is doing is artificial selection. He has a large herd and is selectively breeding it. If he loses some, he has plenty of others. You, on the other hand, have a handful of animals. If you lose some, you have to bring in others from outside your operation to replace them. That's neither sustainable nor efficient, and it certainly isn't artificial selection. It's just a particularly inept form of hobby farming.
1) I was talking about him, not me.

2) You're an idiot.

3) What I am doing IS sustainable from a FEED perspective.  How many times do I have to say that "no inputs" for me means "no COMMERCIAL FEED" inputs.  Geez.
So you acknowledge that you have no sustainable system and are not working towards one.

Got it.
8
Here's another thing that Shapiro gets, but you Hawkinsed past it, or possibly simply stole someone else's quotemine:


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This 21st century view of evolution establishes a reasonable connection between ecological changes, cell and organism responses, widespread genome restructuring, and the rapid emergence of adaptive inventions. It also answers the objections to conventional theory raised by intelligent design advocates, because evolution by natural genetic engineering has the capacity to generate complex novelties. In other words, our best defense against anti-science obscurantism comes from the study of mobile DNA because that is the subject that has most significantly transformed evolution from natural history into a vibrant empirical science.

It's in the paragraph directly below the one you cited.

oh yeah I've read that too. It's irrelevant though because it's just Shapiro's speculation. In science, you see, observation and evidence is much more interesting than speculation.
If that's just speculation, so is the paragraph you quoted.
9
Wingnuts Magic Up Novel Legal Theory About Michael Flynn's Innocence, Are Pathetic :)

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EXCEPT, Judge Sullivan enters the exact same order into the record on every criminal case he hears. And when he entered the order on the 16th, he made a notation that said, Ooops, my clerk accidentally used an old version of this document. Just updating, NBD.



But that doesn't gibe with Byron York's theory that Mike Flynn was coerced into pleading guilty and now the government will have to turn over evidence proving he never committed those one million crimes. So York just left that part out. 
Hahaha ... Jon's about 5 pages behind ...
That article was posted yesterday.  Have you acknowledged that there is no substance to this Flynn drug dream?
10
Wingnuts Magic Up Novel Legal Theory About Michael Flynn's Innocence, Are Pathetic :)

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EXCEPT, Judge Sullivan enters the exact same order into the record on every criminal case he hears. And when he entered the order on the 16th, he made a notation that said, Ooops, my clerk accidentally used an old version of this document. Just updating, NBD.



But that doesn't gibe with Byron York's theory that Mike Flynn was coerced into pleading guilty and now the government will have to turn over evidence proving he never committed those one million crimes. So York just left that part out. 
11
600 years ago in North America was anyone doing forage analysis for the buffalo?  Planting specific varieties for them to eat? 

Answer is "No"

Did the buffalo suffer for it?

I doubt it.
Of course they did.  They weren't being dragged around in cages.
12
Lol

:facepalm:

You say all these things because of your massive brainwashing by conventional animal husbandry people.

I remember sitting through Greg Judy's classes and he was telling about when he first began to implement the principles of HMG. Like your neighbor with the Sheep, he jumped in and started having success thanks to the guidance of Ian mitchell-innes. Ian lived in South Africa and would visit Greg once or twice a year to Mentor him.  Every time Ian would visit, he would ask Greg why are you doing ________?  Greg said at first it kind of ticked him off, but then he never could come up with a good answer as to why he was doing that particular thing ( like hoof trimming ) and over time he began to realize just how much he had been conditioned by conventional animal husbandry people.
Preaching. That's all.
I'll ask Petey why they trim all the hooves, next time I see him.
good idea. Then call Greg Judy or Joe hopping and ask them why they do NOT trim hooves. Then you will have ALL the data not just some of it which supports your preferred narrative.

See?  The answer to the question "why don't you trim your sheeps hooves?"  is NOT "ALL the data not just some of it". 

An EXPLANATION is not DATA.  It is a THEORY that someone puts forward to ACCOUNT for their data.
You're mistaken that I don't know the difference ... what you don't realize is that I just move faster than you do. 

I'll back up and slow down a bit so you can follow ...

I told Sea Star to I will call her sheep friend to ask about hoof trimming.  When she speaks I speak to them, she I will receive both data and analysis - namely "Petey's" analysis of his data.  I also told her will to call Greg or Joe.  If she does I do, she I will receive different data and different analyses of that different data. 

At that point, she I will be better positioned to try to form an opinion about hoof trimming.
FIFY.

(Since you won't figure it out, I'm pointing out that you have neither data nor analyisis.)
13
How do you intend to validate your model? Any results are meaningless without validation.
14
Spoiler (click to show/hide)

I think it will demonstrate the superiority of an animal foods based system. But if I'm wrong ... Ok. I'm wrong several times a day. It's part of science.
No simulation demonstrates anything about the real world unless calibrated by and checked against known real world conditions. Even then you should be cautious about what the results mean.

Or, to be more Pingu'y, a simulation is a model. All models are "false" in the sense that they cannot capture every aspect of the modeled system. Some models are close enough to be useful. Some aren't.

Is your proposed simulation close enough to be useful? If yes, how do you know?
15
No uncool... the assumptions have to be grounded in reality.

Can't invoke magic.
An island just like Missouri is magic.
16
The devil - they say - is in the details.
As in Lake K.
17
I was more concerned when Obama sent a planeload of cash to the Iranians
... even though it was their money?

It was a blackmail/ransom payout, no matter how you wish to spin it. With the sanctions in place, it was no longer their money.
Sorry, no, it was legally their money.
18
You people are lazy.  Get up early like I do and READ.

Bullshit Dave. You haven't answered my question. You've answered what happens to animals and other ecosystems under a hypothetical small-scale project, but you refuse to answer what happens in your 'large scale, save the planet, type plan'.
Which is the question I want you to answer.

I'm thinking that your large scale plan requires the wholesale destruction of any ecosystems not compatible with your 'oak savannah' style farm. Refute me.
Dunno.  But let's to get to first base first, ok?
If we ever do, it'll be too late. That's why people plan. To avoid disasters such as what you propose.
19
That was not my answer.  Keep looking.

Well, seeing as Dave refuses to answer, and refuses to link to his previous "answer", I think we can safely assume that Dave's grand plan requires the destruction of most of the existing ecosystems on earth. and the replacement of them with "oak savannah" style farmland.

So the answer as to where lions and tigers and bears live is .............nowhere.
You're wrong. Keep looking.


No Dave. Stop being such a chickenshit. Link to it.
Find it yourself.  Try to keep up. Why do you care anyway? 

Truth matters... to us.

To you not so much.
20
You people are lazy.  Get up early like I do and READ.
I read everything you posted after Martin's question.

I posted everything you posted after Martin's question in two messages.

Everyone can see you are lying. You know your fantasy requires destroying many, many environments and species. You are ashamed to admit that. So you lie in a pathetic and futile attempt to avoid admitting it.

Maybe you are so delusional that you think you did answer.

Everyone else knows the truth. None of us are fooled.
21
And here's everything you've posted today:

You're wrong.  As usual.
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Why wouldn't you use a 40 acre plot that they've already cut and abandoned?
Sure if fertility is enough to establish grasses. 
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And, if you cut 40 out of a million, probably not. But for sure they won't live on that 40 acres.
  True, but remember I'm not planning on clear cutting vast swaths like the conventional cattle ranchers are doing.  I'm suggesting small plots dotted like patchwork in the existing rainforest so I don't know why the wildlife would not still have plenty of habitat.
Quote
Also, you could stock how many cows on well managed 40 acres? 30? More?
I don't know.  But I did hear recently of a lady in Maine who has a large section of her pasture that produces 11 tons of dry matter per year.  That's freaking 22,000 lbs - enough for about 2 cows.  If I could achieve half of that forage production then 40 acres = 40 cows.  But I doubt I would run cows at all.  Or maybe just a few for some milk.  I am envisioning sheep and hogs for meat and chickens for eggs.
Quote
Are the wai wai lactose tolerant?
No idea, but I doubt it.  You guys have drunk some weird Koolaid on that issue.
Maine? Fucking MAINE? Goodamn you are an idiot.
Actually ... New York ... I had that wrong.  What have you got against "fucking Maine"?
You're wrong.  As usual.
So what does Judy think of your operation?  Surely you've run it past the master?
Of course.  He said "Sounds like you have figured out the goat operation quite well."
Why do YOU care?
You're wrong.  As usual.
So what does Judy think of your operation?  Surely you've run it past the master?
Of course.  He said "Sounds like you have figured out the goat operation quite well."

Why do YOU care?

Oh, is that what he said?  "Sounds like"?  Sounds decidedly vague to me.

Did you fully describe the caged goats, mechanically winched around a field?
I answered your question.  Now answer mine.  Why do you care?
Dave. Nobody cares about your "trials", or these small scale projects you imagine you'll do one day.

Your plan to save the world requires that your ideas be scaled up and implemented pretty well everywhere, yes? (eg: Your maths).
What we want to know is under this long term plan of yours, what happens to the lions and tigers and bears.

You can't say that your work is too minor in scale to affect wildlife populations, and then argue that it should be applied everywhere.
That's not a logical leap.

If your plan is to have a few acres in Missouri and a few in Guyana, then nobody is really going to care about your impact on ecosystems.
But that's not your plan is it? eg: " I would advocate for this general configuration everywhere on earth that it's possible" - Dave.
So the question is what happens to the existing ecosystems under that plan?
And that seems to be a question you really don't want to answer.
Dave?
I answered this.  If you can't keep up, go back and review.

Of course you have no answer, so squid ink and lying is your recourse.


22
You're lying. None of your posts after Martin's addressed the issue. Note that Martin posted his message after your previous idiotic response saying that your Missouri hell-hole and any shitstorms you create in Guyana won't be big enough to kill off all that wildlife.

For your convenience, here's everything you posted yesterday after Martin's message:

Quote
Why wouldn't you use a 40 acre plot that they've already cut and abandoned?
Sure if fertility is enough to establish grasses. 
Quote
And, if you cut 40 out of a million, probably not. But for sure they won't live on that 40 acres.
  True, but remember I'm not planning on clear cutting vast swaths like the conventional cattle ranchers are doing.  I'm suggesting small plots dotted like patchwork in the existing rainforest so I don't know why the wildlife would not still have plenty of habitat.
Quote
Also, you could stock how many cows on well managed 40 acres? 30? More?
I don't know.  But I did hear recently of a lady in Maine who has a large section of her pasture that produces 11 tons of dry matter per year.  That's freaking 22,000 lbs - enough for about 2 cows.  If I could achieve half of that forage production then 40 acres = 40 cows.  But I doubt I would run cows at all.  Or maybe just a few for some milk.  I am envisioning sheep and hogs for meat and chickens for eggs.
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Are the wai wai lactose tolerant?
No idea, but I doubt it.  You guys have drunk some weird Koolaid on that issue.
Spoiler (click to show/hide)
They are pretty much guaranteed to be.
Bullshit.  You hang around octohetters too much.  Step into the real world sometime.

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Also, chickens don't need to be moved. There is no real benefit to doing so in general. 
Joel Salatin moves them to follow cows.  But if I don't have cows ... then yeah ...

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You could build some coops and then there would be eggs and chicken.

Eta: I mean, you don't have to clear a patch of forest for them.
OK
Why have the Wai Wai been asking for your help for a long time when as you say, you haven't got some first hand experience under your belt?
Have you been bullshitting them about your 'expertise' too?
Alfonso - for once in his life - asks an intelligent question - woo hoo! Pinching myself.  Can this be real? I was a logical choice to ask for help, not because I knew lots about agriculture at that time, but because I was willing to learn and of course they knew me already and I'm decent with their native language.  Also I was willing to make an attempt to help them which I'm in the process of doing by learning and experimenting.
Raffy enjoys talking to himself.
Continued on next rock...
23
Lawsuit Filed Against Chuck C. Johnson, Jim Hoft, Paul Nehlen, Gavin McInnes and Others for Falsely Linking Michigan Men to Charlottesville Attack

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After last year's white supremacist rally in Charlottesville, Virginia, at which counter-protester Heather Heyer was murdered when one of the racists deliberately drove a car into a crowd, we reported that a slew of right wing sites immediately and recklessly rushed out articles identifying the wrong person as the perpetrator of the attack.

These irresponsible bloggers included our old pal Chuck C. Johnson (who is NOT ME, and is not really my "pal") and Jim Hoft (the fabled Stupidest Man on the Internet). And from those two sites the fake story quickly spread throughout the right wing noise network.

Both of these far right bloggers soon deleted their posts, but of course they know very well that once they put this malicious nonsense out on the Internet, the right wing mob will take it and run with it, and there's nothing anyone can do to stop or debunk it from that point; it becomes an article of faith and takes on a life of its own.

...
And this week, they filed a lawsuit against an entire group of these people, including Chuck C. Johnson, Jim Hoft, Gavin McInnes and Paul Ryan's white nationalist primary challenger Paul Nehlen, seeking damages for defamation, invasion of privacy and intentional infliction of emotional distress.
 
Dave gets competition.
Dave's a big fan of Hoft.
24
Digby is well worth reading.
 
Yes Houston. We have a big problem.

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The best case scenario is that the president of the United States was an unwitting dupe but is so deranged and ignorant that he refuses to take action to prevent this from happening in the future and is actively covering up the scandal to assuage his fragile ego. And in the process, he's implicating himself in the scandal after the fact.
25
Lawsuit Filed Against Chuck C. Johnson, Jim Hoft, Paul Nehlen, Gavin McInnes and Others for Falsely Linking Michigan Men to Charlottesville Attack

Quote
After last year's white supremacist rally in Charlottesville, Virginia, at which counter-protester Heather Heyer was murdered when one of the racists deliberately drove a car into a crowd, we reported that a slew of right wing sites immediately and recklessly rushed out articles identifying the wrong person as the perpetrator of the attack.

These irresponsible bloggers included our old pal Chuck C. Johnson (who is NOT ME, and is not really my "pal") and Jim Hoft (the fabled Stupidest Man on the Internet). And from those two sites the fake story quickly spread throughout the right wing noise network.

Both of these far right bloggers soon deleted their posts, but of course they know very well that once they put this malicious nonsense out on the Internet, the right wing mob will take it and run with it, and there's nothing anyone can do to stop or debunk it from that point; it becomes an article of faith and takes on a life of its own.

...
And this week, they filed a lawsuit against an entire group of these people, including Chuck C. Johnson, Jim Hoft, Gavin McInnes and Paul Ryan's white nationalist primary challenger Paul Nehlen, seeking damages for defamation, invasion of privacy and intentional infliction of emotional distress.