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Messages - VoxRat

1
...
What we biochemists mean by "error" in nucleic acid polymerization is the incorporation of nucleotide(s) in the copy different from those in the template from which the copy is being made.

You're welcome.

VoxRat, PhD in Biochemistry.
Which includes, for example, reversions, right?
Yep
2
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.
Thanks for asking.
What we biochemists mean by "error" in nucleic acid polymerization is the incorporation of nucleotide(s) in the copy different from those in the template from which the copy is being made.

You're welcome.

VoxRat, PhD in Biochemistry.
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.
:badger:
4
Of course it doesn't answer "the question" as to what DAVE means by "error". 

Dave himself doesn't even know what he means, any more than he knows what he means by "random".
I'm pretty sure it boils down to:
The sequence ordained by God is the "correct" sequence.
Copies of the sequence that differ from that are "incorrect", "mistakes", "errors"...
But, having just cited Shapiro, and written:
This is a science forum.
... he has to avoid honestly answering the question at all costs.

5
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

Dave: try expressing what YOU think - your OWN point - instead of just linking to papers you clearly do not understand.
The linked paper, incidentally, does NOT answer the question.

I use expressions like "error-prone polymerase" all the time.
But, unlike Hawkins, I can tell you exactly what my definition of "error" is in that context.
6
It could be a "mistake" or "error", I suppose.
Depending on your definition of "mistake" or "error".
What's yours? 

:icare:
Stupid ass question.
Actually, it was a rhetorical question.
Because we all know you don't have an answer.
7
It could be a "mistake" or "error", I suppose.
Depending on your definition of "mistake" or "error".
What's yours? 

:icare:
8
Pingu: "mutations aren't mistakes."
Aaaaaand ... there it is.
The entirely predictable Hawkins quote mine.
(And Hawkins conveniently forgets how to use the quote function).

We've been through this.  They aren't "mistakes".  They are DIFFERENCES.  They are only "mistakes" in the METAPHORICAL sense that if you write "behavior" and I quote you and write "behaviour", I have "miscopied" you - but the result is just as valid as the original.  Mine is not a "faithful copy". That doesn't mean it's "a mistake".

9
Smearing what kids? Give me an example. I think you guys are just smoking dope again.
Take it up with  Lauren Hogg.
11
It appears to me that some extremely intelligent "made evolution" - which, rightly defined, could be called "pre-programmed adaptability" ...
You are in no position to set definitions in a subject of which you are profoundly ignorant.
Quote
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. 
No it doesn't.

See how easy it is to make unsupported assertions?
12
But you would also be taking the analogy much too far.
... which was pretty much the point of the article Hawkins quoted in the OP.

Hence the own-goal.  :cheer:
13
If evolution doesn't need God to exist, what is he even for?
You think gays are going to get to hell by themselves?
14
I know for a fact that functional software can be made by people who don't understand what they are doing.
I am living proof of that!  :wave:
15
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?
You miss the point.
(Probably intentionally. That's part of the militant ignorance, as opposed to plain old ignorance, thing.)

ST is talking about complex solutions in lieu of obviously simpler solutions.
He spelled out exactly what he's talking about:
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.
You, of course, (militantly) ignored that.
16
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 ...
Before anyone could even conceivably answer this "question" (such as it is) you would need to clarify. A lot.
For starters:
- Who's "we" ?
- What does it mean for "us" (whoever "we" are) to be "familiar" ? With either the 1.5% or the 98.5% ? Do you assume that no one knows anything about non-coding DNA?
17
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

Thanks for proving my point.
Nothing in there is anything remotely like your profoundly dishonest (mis)characterization:
Quote
organisms don't operate very well.

18
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.
::)  Pure preaching.  And pretty stupid preaching, at that.
19
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
20
You are wallowing in ignorance while pretending to be knowledgeable enough to judge biological software.
Dave.

Get a grip.

You have never cracked a book on introductory genetics.
not quite true, but I know what you are getting at. And what you are getting at is irrelevant and here's why...

There are plenty of people who have cracked these sorts of introductory textbooks and gone much further an example of which I quoted this morning. These people are making the point that Craig Venter is basing his project upon his knowledge of a only about 1.5% of the human genome.

I've got news for you... Any fourth grader whether he has cracked an introductory textbook on genetics or not... Can observe that a person who proclaims that something is poorly designed when they don't have the first clue about 98.5% of it ...

Is just about the best textbook example of arrogance combined with stupidity that you can find anywhere.
This is just about the best textbook example of a strawman argument (combined with Hawkins-grade arrogance and stupidity)  you can find anywhere.
21
You are wallowing in ignorance while pretending to be knowledgeable enough to judge biological software.
Dave.

Get a grip.

You have never cracked a book on introductory genetics.
You are in no position to opine about others' "ignorance" on the subject.
22

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/

Congratulations on your own-goal!   :golfclap:  :banana:  :cheer:  :happydance:  :cheer:  :banana:  :golfclap:
23
Smearing what kids? Give me an example. I think you guys are just smoking dope again.
People this clueless should not be allowed to vote.
24
He woo hoos sex with kids so not that far out of the realm of possibility he would lol @ killing them too.
this is a great example of the mental debauchery that many people who post here have. When you lie to yourself and to everyone else constantly, then you say nonsensical things like this. The truth is I woohoo with those who are woo-hooing ( the Young Bride and her elderly groom for example ) and I am sympathetic toward those who are not woo-hooing such as all those poor families that were victims of the shooting.

Bullshit. You're, afaik, still reading and applauding some of the people who've been smearing those kids for days.
THIS   is the point.
25
mental debauchery
::)

wtf is this moronic phrase even supposed to mean ?