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Messages - Dave Hawkins

2
Something just happened on this topic just south of my hometown that really pisses me off. Namely, a lovely (from my perspective) piece of land of about 138 Acres got sold to a stupid row crop farmer who promptly tilled up all that beautiful forage in preparation to plant corn and soybeans.  How much did it sell for? God only knows but I'm sure it was at least $5,000 an acre. And the whole concept of land purchasing is stupid anyway. We should Institute County rules that prevent this sort of thing from happening. I want to work on that.
3
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. Jesus Christ you're an idiot.

Why are we even talking about this stupid shit anyway?

This Thread is about the economics of saving Agriculture and I'm really interested in trying to figure out how to enable people to recolonize the land without breaking the bank.
4
Hey Dave. Did you forget this post? Or are you badgering again?

I can safely say as the father of two expert bowhunting sons... That this is a poorly designed bow and arrow ... they would not be kill anything with this. WTF was the designer thinking!?



I cannot get this dang image to show
There we go ... it was an issue with my phone.

Anyway, do you see my point?
Yes, Dave. Your point is that you think we're idiots that can't think through the fact that there are differences.

We talked about one principle of programming before: a programmer documentary his code on all levels he thinks someone else will use. A programmer that doesn't is either an inconsiderate programmer, an incompetent programmer, or a hostile programmer.

God didn't document his work on most levels. So which one is he? Inconsiderate, incompetent, or hostile?
Though this is a bit late, I believe the designer of that nerf bow and arrow was not trying to make a lethal weapon for actual hunting and/or warfare but rather to make a play toy bow and arrow that was safe for kids to play like they were hunting or at war. Sort of like kid's cap guns don't really shoot bullets and play swords are made of foam so they don't actually cut things.

Bluffy really is a bluffoon.
That's...kind of his point.
Yes exactly ... An African bushman might see this bow and arrow and think "poor design" (by African bushman bow and arrow standards) because he can tell by looking that he could not kill an animal with it ... Just as Saunt Tonga can tell by looking that "biological software" exhibits "poor design" as well assuming human software writing standards.
You are confusing function and design again. Design is about how the function is achieved. Your bushman is thinking poor function, it will not kill, not poor design.
If a fully functional bushman's bow was made with three times as much material in three times a much time. And being a bow maker, the bushman sees all this, the bushman might well think, OK, it works, but the guy that made it is incompetent.

That's what I mean by bad design.
I'm not confusing anything. If you prefer, consider the bush man seeing a compound bow for the first time. He might think that it's bad design because of all those pulleys and extra lengths of string.

The point is that if he tries to authoritatively assert that it's bad design, he's making a mistake because the truth is he simply doesn't have knowledge about compound bows.

Just like you don't have knowledge about biological software. Or certainly not very much knowledge. None of us do.
5
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.
6
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.
7
It could be a "mistake" or "error", I suppose.
Depending on your definition of "mistake" or "error".
What's yours? 

:icare:
Stupid ass question.

Read this ... https://www.nature.com/scitable/topicpage/dna-replication-and-causes-of-mutation-409
8
You frequently quack like a duck, has any one identified you as an actual duck? No, of course not, because 'quack like a duck' is metaphorical.
I do?
9
Coyotes eat it ...  just like they eat ducks.
10
Looks like a duck.

Walks like a duck.

Quacks like a duck.
11
What we have here is that people like Pingu are

HILARIOUSLY OUT TO LUNCH

in saying that "random mutations are not mistakes"

Hahahahahaa
12
Also, Shapiro ...
Quote
It has been a surprise to learn how thoroughly cells protect themselves against precisely the kinds of accidental genetic change that, according to conventional theory, are the sources of evolutionary variability. http://truthmatters.info/shapiro-buries-naturalism/

"Mutations are not errors" my ass.

Lol

Please drop this nonsense once and for all.

This is a science forum.

Thank you!
13
Pingu: "mutations aren't mistakes."

Ayala:

Quote
Ayala, Francisco J., "The Mechanisms of Evolution," Scientific American, vol. 239 (September 1978), pp. 56-69.
p. 58
"A mutation can be considered an error in the replication of DNA prior to its translation into protein."

Lol
14
Hey Dave. Did you forget this post? Or are you badgering again?

I can safely say as the father of two expert bowhunting sons... That this is a poorly designed bow and arrow ... they would not be kill anything with this. WTF was the designer thinking!?



I cannot get this dang image to show
There we go ... it was an issue with my phone.

Anyway, do you see my point?
Yes, Dave. Your point is that you think we're idiots that can't think through the fact that there are differences.

We talked about one principle of programming before: a programmer documentary his code on all levels he thinks someone else will use. A programmer that doesn't is either an inconsiderate programmer, an incompetent programmer, or a hostile programmer.

God didn't document his work on most levels. So which one is he? Inconsiderate, incompetent, or hostile?
Though this is a bit late, I believe the designer of that nerf bow and arrow was not trying to make a lethal weapon for actual hunting and/or warfare but rather to make a play toy bow and arrow that was safe for kids to play like they were hunting or at war. Sort of like kid's cap guns don't really shoot bullets and play swords are made of foam so they don't actually cut things.

Bluffy really is a bluffoon.
That's...kind of his point.
Yes exactly ... An African bushman might see this bow and arrow and think "poor design" (by African bushman bow and arrow standards) because he can tell by looking that he could not kill an animal with it ... Just as Saunt Tonga can tell by looking that "biological software" exhibits "poor design" as well assuming human software writing standards.
15
No one ever said "ORGANISMS are like code."

It's DNA that's "like code" ... somewhat ... but it's far more sophisticated. 

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

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].

Exactly.  So why are you banging on about "software"?
:facepalm:

Seriously?
16
No one ever said "ORGANISMS are like code."

It's DNA that's "like code" ... somewhat ... but it's far more sophisticated. 

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

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].
17
Does this have to be an Either God Or Evolution question?
Isn't it possible that evolution itself is God's design?
Why would God do things the same way we humans would? I think it is arrogant of any human to claim to understand the mind of God.
Well, if God made evolution, there's not a lot else left for him to do. He could just sit back and watch. Or just leave.
Also, does evolution need creating? If evolution doesn't need God to exist, what is he even for?
It appears to me that some extremely intelligent "made evolution" - which, rightly defined, could be called "pre-programmed adaptability" ... In other words, however organisms came to be (believe what you will) it does indeed appear that they are pre-programmed to adapt to various niches. 
18
Also ... Life is mind numbingly complex ... so ST thinks that's a sign of bad design ...

But many man made items are also quite complex ... does this mean THOSE are bad design too?
19
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?"

I still have not got an answer to this ...
20
Yeah ... organisms don't operate very well ... if God would just update the software ...
No one said "organisms don't operate very well".
Or anything like that.

Your strawman campaign continues.
It is profoundly dishonest.
Quote

Lolololol
idiot
Ahem.

Yes they DID say that.

Here's the whole convo which you dishonestly omitted part of ...

Quote
Also, this
Quote
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.

Quote
Hahahahahaha

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

Lolololol
More...Quick EditQuote
21
Here is a quick and dirty version, Dave:

First a short preamble:

Biological organisms reproduce themselves, with variance, i.e. offspring are close enough to their parents that we can call it "reproduction" but there are always small differences.  These small variations have lots of different causes, but quite a lot of them are due to the offspring having slightly different DNA sequences to the parent.

Let's for now talk about sexually reproducing organisms to keep things simple-ish.  Sexually reproducing organism produce offspring that have some features of one parent and some features from another.  The combination itself makes them unique. But the combination at genetic level means that sometimes brand-new genetic sequences are generated.  Other mechanisms can also result in novel sequences.

Now for the main point:

As with Joe Hopping's sheep, sometimes a variant will appear with no obvious reproductive advantage or disadvantage to the organism.  Dark, slow-growing hooves for instance, instead of lighter, faster growing hooves.  Because there's no clear advantage or disadvantage, populations of these sheep will have some dark-hooved individuals and some light-hooved ones.  Then a specific population finds itself owned by Joe Hopping.  Now light hooves are seriously disadvantageous, because Hopping doesn't let them breed.  He only breeds from the dark-hooved ones.

But you know this.  You also know that this happens NATURALLY - instead of being owned by Joe Hopping, the sheep may find themselves in a very boggy environment, where their hooves don't wear down easily, and they also trap what my grandmother called gubbins.  So they tend to get infected feet.  So the dark-hooved onces have a reproductive advantage.

In other words, the population genome becomes OPTIMISED for boggy ground by dint of that population mostly bearing the dark-hooved sequence.  Rinse and repeat, over and over, and you end up with shorter/longer horns, thicker/thinner wool etc.

Great system for optimisation.  In the process lots of other not very useful variants appear.  They get weeded out if they are actually harmful, but not if they don't.  They just sit there in the population doing nothing, until the environment changes in a way that they are either useful, in which case they will become more prevalent, or disadvantageous, in which case they will become less so.  Or they may just hang around to delight us with variety.

That method of optimising a genome is not the way a human designer would do it.  There are loads of disadvantages.  You get lots of redundant code.  And you can't transfer good bits of code into other bits of code very easily to get the best of both worlds (sexual reproduction isn't a very efficient means of horizontal transfer).  And you waste a lot of sheep and time.

But it doesn't matter because you have plenty of sheep and time.

A human designer doesn't.  So a human designer has to figure out what is needed, as efficiently as possible.  She has to decide on a single solution quite quickly - she can't afford to experiment with weird and unlikely solutions of no obvious immediate benefit.  She doesn't want to write a whole bunch of redundant code. 

However, what she can do, is easily splice bits of code in from some other programme.  She can make the code quite modular in fact, and call on lots of existing functions, many developed by different teams for different purposes.  And she expects them to be easily understood and readable, and not be full of irrelevant extra stuff.

So to her, a sheep genome, even of one of Hopping's sheep, would look like "bad code".  Lots of useless stuff, some of it potentially useful for some non-obvious purpose, lots of it simple leftover junk.  And she'd find it was virtually impossible to transfer any of it to anything other than a subsequent version of the code.  No swapping anything other than tiny bits over into somebody else's code.

In other words: human software looks like it's been designed by and for human designers.  Biological genomes look like they evolved.

The first shows evidence of the limitations and non-limitations of human designers.  the second shows evidence of the limitations and non-limitations of evolution.

Which is why most people find the ID argument pretty flawed.  The very things that DON'T look like the way humans design things are the very things that are TYPICAL of things that have been optimised by evolution.  Which is a pretty good system.
Some of what you say here is true.  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.  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). 

The more we learn about genomes, the more we realize that this amazing adaptive system that your describe HAS ALWAYS BEEN THERE.  IOW, we don't have any evidence of it having NOT been there ... EVER.  Any speculation that it wasn't at some point in the past is just that ... speculation ... and pretty stupid speculation at that.  That idea flies in the face of all reason and logic and experience.
22
Oh my God ... the stupidity ... it burns!!
23
"There is a new class of software that is quite a bit more like biological systems."

Wait.

Why?

I thought biological software was "bad design".

Wow.
24
I missed this one ...

"Complexity is a sign of bad design."

Hahahahahahahahahahahaha

So God's unimaginably complex design that allows sunlight to be converted into grass which in turn is converted into meat, milk and eggs is ...

DRUM ROLL

Bad design.

Oh my sides!!!!!!!!!!!!!!!!!!!!!!!!!
25

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