[muglo] Re: 100% [OT] Biology

>Have faith in the fact biology is more complex
>than what we currently understand.  If it was that simple, we wouldn't have
>to just place blanket attempts at restrictions of practices, rather than
>eliminating the issue up front.

You defeat your own arguments with this statement -- biology cannot be both 
"more complex than what we currently understand" yet simultaneously 
"Genetics is not an unstable system. Not by a long shot."

You need to remember that things get massively simplified at the undergrad 
level -- take your training should act as a basis for further reading. Until 
you get into the primary literature nearly *everything* you learned suffers 
from "exceptions to the rule" rule ("There's an exception to every rule, 
except this one").

>Not at all.  Since it's a multivariable process, you can't assume anything.
>How do you assume how it's spread?  What is the carrier?

Carrier = contaminated ruminent feed resulting from the rendering 
(processing) of a BSE-"infected" animal into food that is then fed to other 
BSE-susceptible ruminents. I should remind you that the mode of action of 
the "prion" protein is to refold the non-prion version of the protein into 
the prion version -- since the "regular" protein is produced by the cells, 
there's a never-ending supply of normal proteins to be refolded into the 
disease form. Eliminate the opportunity for the prion to be passed to 
another animal through eating or inheritance (if that works) and you stop 
the disease. Period. *No* risk of spread like in nearly all viruses, 
bacteria, animals, plants and fungi (since all can cause transmissible 
disease)!

Spread = willing seller (or oblivious or stupid or corrupt) selling 
contaminated feed to willing buyer. If willing (or oblivious or stupid or 
corrupt) buyer is in Nebraska and seller is in Yorkshire then transaction is 
completed and contaminated feed is transferred.

>Your parsimonious
>explanation?  Rather weak.

Is this not what the inquiry into the BSE case has concluded? Hmm. Weak?

>You'd get no research funding with that
>explanation.  Perhaps you've forgotten the Scientific Model.

Scientific Model -- you run the risk of reifying your terminology when you 
start to capitalise words (just like parts of the Communist party in Russia 
were essentially an atheist religion)!

>"Transmitted through direct maternal through non-genetic inheritance".  Um,
>ok.  You'll have to explain non-genetic inheritance.  As well, folding
>proteins.  At time of creation or like co-enzymes?

Genetic inheritance is usually reserved for DNA-based (gene-based) 
inheritance of traits. Passing down of a prion from mother to offspring 
would be non-genetic inheritance since it's not in the form of a gene 
(unless it's a genetic form like Kreuzefeld-Jacob disease... although, 
perhaps that too is non-genetic (we're not exactly cannibals ;)). Lamarkian 
inheritance (if you'll recall your genetics... which probably told you that 
Lamarkian inheritance was *wrong*... but that too turns out to be too 
comprehensive a generalisation) is a little more ambiguous at times -- 
temperature controlled inheritance of traits is non-genetic. Methylation of 
DNA is also ambiguous. Yes, it is the DNA that's modified & inherited, but 
the methylation can be removed or added in subsequent generations 
(methylation is a commonly used mechanism to control the expression of genes 
in *subsequent* generations. I seem to remember a recent study in Sweden 
looking at weights/income (or something like that) and ended up finding some 
Lamarkian effects... this was an epidemiological study IIRC so they wouldn't 
find the mech'm)

PS methylation can control the expression of genes by preventing 
transcription -- the "transcriptases" (you may notice that I prefer to 
bastardise enzyme names rather than use the originals... a habit I picked up 
in 2nd year since most people understand that better than the names (e.g. 
DNA polymerase) ;). Anyway, the transcriptases can't bind to the DNA to 
transcribe it. Methylation is often transitory and does not survive more 
than one generation but stable systems have been uncovered (flax... a stable 
methylated system that arose in the 1950s has persisted).

> > What stats? What stable system? Genetics is an *unstable* system -- the
> > system is full of errors and full of error correction, ESPECIALLY as an
> > organism ages! There's just a rather high level of tolerance (how do you
> > expect evolution to happen if there's nothing to select (Lamarkian bunk 
>not
> > withstanding... though, there are *some* case where Lamarkian 
>inheritance is
> > possible (but not how he thought)) ;).
>
>Genetics is not an unstable system.  Not by a long shot.  It's amazing how
>students learn how all of this works, and how we have a small percentage of
>mishaps and we end up studying how the whole system works by studying our
>mutations and such, then all of a sudden, they think it's the mutations 
>that
>are the majority.  If that was the case, we wouldn't have organisms, just
>chaos.

Depends... mutations are extremely common. Error correction and fault 
tolerance make the difference. The reason we can construct phylogenies of 
organisms only a few decades old is the very fact that mutation is quite 
common and fault tolerance allows it to persist (remember your wobbly 
triplet codons?)

>BTW, the ribosome has 100% to do with how proteins fold.  Tertiary 
>structure
>has a natural static formation, changeable or not.

Hahahahahaha. You didn't go into biochemistry and genetics past year 2, did 
you? there's *nothing* static about it (that thinking's not fit for more 
than a 2nd year course... and in recent years (probably 97 or 98) shouldn't 
be taught at anything more than a 1st year level... well except for in 
science for non-science students classes)). Some proteins are capable of 
adopting the right 3d (or even quartenary) structure without external help, 
but there are many more that require the help of these folding proteins 
(their name escapes me off the top of my head) to adopt the correct 
structure. In some cases post-translational modification is necessary (e.g. 
adding/removing functional groups like CH3, disulphide bridges (remember 
your hemoglobin?) or benzene or something like that) to allow the protein to 
fold, in other cases, the proteins need to be "forced" into the right 
structure. Sometimes the pH plays a role (salts on the functional groups on 
the amino acids). Some folding proteins actually change the pH of their 
active sites (or even cavities) thus allowing the proteins to adopt the 
right structure before being booted into the wide-world of the 
cells/intracellular space.

Do you know about the Folding@home project? This project demonstrates the 
non-static nature of the structure of a protein. They seek to simulate the 
folding and re-folding of proteins *billions* of times -- this is what 
happens in natural systems (remember your x-ray crystallography?), just at 
extremely rapid rates. When that rapid folding and re-folding doesn't work 
right off the bat is when post-translation modification or folding proteins 
come into the mix.

This is why denaturing (heat, chemical, pH, whatever) works. Denaturing 
destroys tertiary structure & often post-translation modifications. After 
denaturing, some proteins can adopt their tertiary structure, but many more 
can't -- their sequences are still intact though (well, depends).

Anyway, prions function as folding proteins (with the purpose of folding 
their non-prion selves into prions).

Plus, the reason I brought up the stochastisity is that claims of we "know" 
what's going on in biotechnology is a patent lie. *Sometimes* we can 
reasonably say we know, but often enough it's not much more than an educated 
guess.

>100%, not some, are made at the ribosome and assume a structure outside of
>that translation.  I'm fully aware of proteomics.  What program do you 
>think
>I'm appying to?  Hehe.  We have one program at Ivey based on this.  It has
>been alive for more than 20 years now

(hmm. that's interesting since proteomics only came into being in the late 
1990s).

>Wow, you have a real problem with the real world.  Perhaps you should get
>out into the world of application and see how things work.  I'm talking
>domesticated corn.  The stuff you buy.  Go to Loblaws.  Or, unless, you
>harvest your own wild corn for some strange reason.  I find it ironic 
>people
>buy products that have been changed so much, consider it 'organic' or
>somehow 'good product' and have no idea it's been modified through normal
>unnatural selection by farmers.

The difference being that selection by farmers was not through the 
introduction of genes 100% foreign to the organisms in question, and given 
what we know about interaction of protein systems it is irresponsible to 
move a technology this rapidly. I failed to expand on this in a previous 
e-mail. Biotech certainly won't go away -- we're in no risk of losing the 
technology -- and it's not something that's going to "save the world". In 
that case, we should be cautious and judicious in allowing its use until 
such time as we can be reasonably certain we won't see a natural 
catastrophe.

The more I see you write, the more I realise you are driven by ideology 
sprinkled with an undergrads understanding of biology.

>varieties, I wouldn't call safe, nor practical.  One mad cow in Canada did
>NOT dictate banning of Canadian beef through other government organizations
>outside this country, no more than SARS should cut Toronto off people's
>travel lists.  Yet another public service organization, the WHO seriously
>messed up.

... this is a multi-faceted function of the media (fear, fear, fear, hype) 
and precaution in the face of uncertainty (good -- something completely 
ignored by corporations and gov'ts). The media is pretty much useless since 
they feed off hype (they're useful to get info out but they do as much 
damage as good). The WHO did the correct thing FOR ONCE by applying the 
precautionary principle. It's better to be safe than sorry. This disease was 
one of the most virulent deadly viruses to hit Canada -- the fact that it 
spread so rapidly was a cause for concern. (though, yes, driving is a much 
more deadly and dangerous activity).

Who messed up were Ontario and Toronto for getting Ontario *off* the list 
before things were properly under control, only to be put on the advisory 
when it was shown we weren't in control (thus, adding to the PR woes).

> > Ah well, the fun that biology becomes when you add the reification and
> > arrogance of the marketing departments -- uncertainty be damned. We 
>*know*
> > what's going on. Not we *think* we know what's going on.
>
>Which is more responsible?  Consumer or Marketing Department?  How do you

Both! The problem is that the marketing department has information that the 
consumer never knows until a scandal hits the fan. The consumer has a duty 
to stay informed, but if they aren't provided with information to make 
informed decisions their hands are tied (e.g. labelling of GM foods).

>explain to people that have no clue that genetics was used to increase the
>head retention on a beer, without them thinking David Suzuki should be
>brought in to fight the monster making?

Consider this question:
Do normal tomatoes have genes?
Do genetically modified tomatoes have genes?

This was a question asked a few years back in Canada/US/parts of Europe. Far 
too many people answered No (or don't know) to the first question but Yes to 
the second.

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