Holy Hallucinations 23

Uploaded by TheLivingDinosaur on 16.05.2011

This is a response to NephilimFree’s video, “Overlapping & Embedded Genes.”
Hello again, Neph! It’s been a while since I addressed any of your malodorous videos
because I felt it only fair to let you recover from the double-fisting I gave you in Holy
Hallucinations 9 and 10. But now that hopefully feeling a little less dilated, I thought it
has high time that I paid you a friendly visit and put you straight on one or two little
inaccuracies that I found in your video regarding the nature of overlapping genes.
Now, anyone who’s had the misfortune and intestinal fortitude to watch one of your
originals from start to finish will already know of your prodigious talent for taking
ten minutes to haphazardly stumble through what can be said in two. As a result there
may be some repetition in the clips I’m going to show from your video, but that seemed
to be the only way in which I could present the occasional new fecal nugget that you intermittently
introduced during your seemingly endless regurgitation of the same point.
But before I play it, you should note that if you happen to think you’re sounding a
little more eloquent than usual, it’s because I took the time to edit out the ubiquitous
pregnant pauses that intersperse your crapto-didactic prose like peanuts in a squirrel turd. It’s
hard to watch your videos without repeatedly banging your head against the keyboard until
you ears bleed Neph, and so I decided to do my best to shield my subscribers from sharing
the pain. Take my advice; if you’re doing that because
you’re laboring under the impression that it makes you sound thoughtful or intelligent
- then you’re wrong, because the effect’s eerily reminiscent of an intellectually impaired,
lobotomized chimpanzee with a concussion. And if you’re not doing it deliberately
then might I suggest a script, an audio processor and just a small modicum of pride in your
work? Radical thoughts, I know Neph, but they really will help to alleviate the impression
that you’re moonlighting as a stand-in for Forrest Gump.
So now that I’ve finished impugning your intelligence, let’s get onto the part where
I factually demonstrate that these weren’t ad hominem attacks but rather a reasonably
accurate description of observable reality. You may want to go and find something to bite
down on while I play the first clip, Neph, because this is going sting a little.
"I explained to her that one of the problems with the idea that random genetic mutations
has developed in the genome of all the life forms of the Earth, and is the stuff of life
for evolution, is the fact that we have discovered that genes are often overlapping and embedded."
OK, Neph, now that we have the basis of your thesis, I’ll take a little time to describe
the general structure of eukaryotic genes. This’ll make it somewhat easier for anyone
watching this video to follow what I’m saying when I get to pointing out exactly and precisely
why you’re full of crap. In general bacterial genes are stretches of
DNA containing an uninterrupted linear sequence of coding information for their respective
proteins. By contrast, most mammalian genes aren’t contiguous and their coding regions
are broken up by islands of non-coding sequence known as introns.
After transcription into RNA, the exons containing the coding information need to be joined by
removal of introns in a process named splicing that occurs in structures named spliceosomes,
and can be envisaged as being akin to excising adverts from a movie before watching it.
This mature messenger RNA of the fused exons, can then be translated into the final protein
by the ribosomes. Since the genetic code is read in triplet form, where a codon of three
consecutive bases represents one amino acid in the encoded protein, each mRNA can be read
in three potential “reading frames” depending on where translation is actually initiated.
The actual region of translation is delineated by “stop” and “start” codons. Since
these are seldom located at the ends of the transcript, not all of the original exonic
material codes for protein, and the non-coding ends are named the 5-prime and 3-prime untranslated
regions. So now that I’ve laid the groundwork, let’s
get on and take at look at what kind of monumental lies a creationist can conjure out of thin
air by just reading an abstract or two, praying to his ephemeral special friend for inspiration
and willfully ignoring anything that even vaguely resembles a fact.
But before I play the first one, Neph, I was curious by what you meant by the phrase “we
have discovered” when referring to overlapping genes? In fact, you seemed to be very fond
of using this particular conjunction in this video, and if you don’t believe me, then
take a look at this: "We will continue to discover…we have discovered…so
far we have discovered…we may discover…we continue to discover…we’ve discovered…we
continue to discover." Of course the reality Neph, is that you couldn’t
discover your own arse in the dark with both hands, let alone anything in the field of
molecular genetics. I found this particularly galling because the people who actually did
the discovering that you’re referring to are the same people who’d piss their pants
with laughter if they ever heard you ignorantly opining on the subject that they’ve spent
years to decades working in. I’ve said it before and I’ll say it again:
your two years of typing “evolution is a lie” into Google and voraciously lapping
up anything it spat back at you like a pig at a trough full of swill doesn’t make you
an expert in anything other than dishonesty and gullibility. The quality of your online
education’s evident every time you open your mouth, and no more so than in the next
clip. "This illustration demonstrates why all genetic
mutations cause degratory effects to the genome’s code. Because if a random genetic mutation
which affects this portion of the gene takes place it will effect this gene. So even if
we were to find that a genetic mutation provided some imagined benefit to this gene, which
is exceedingly rare, it is almost certain that it would cause degratory effects to this
one. Because genes are overlapping and embedded, random genetic mutations typically effect
more than one gene at a time." I was puzzled when I first saw this, Neph,
because the figure you’re referring to isn’t annotated in English. It turns out there is
a good reason, and that’s because you found it on a Finnish creationist website. It seems
that you’re broadening your horizons, Neph - which is nice, since all other indications
are that you really don’t get out that much. Now, this diagram of yours bears no semblance
to any genetic locus that I’ve been able to find, and since your Eurotrash webshite
of course didn’t give any indication of a primary source for the figure, I thinks
it’s safe to assume that it’s been concocted for the sole purpose of allowing shamelessly
dishonest reptiles like you to misrepresent the complexity of overlapping genes.
Your little artistic interpretation, though, does illustrate the basic concept, and that
is of a genetic locus containing two or more genes that share at least some of the same
physical sequence. An overlapping gene can reside on the same strand of DNA as its partner
and be in the same or different reading frame or, more commonly, on the opposite antisense
stand. Because of the anti-parallel structure of
the DNA helix, same-strand overlaps always run in the same direction, while anti-sense
overlaps can run head-to-head or tail-to-tail. Additionally one gene can be embedded entirely
within another and when it resides within only one of its partner’s introns it’s
referred to as nested. Now, despite your mendacious assertions, Neph,
there are many reasons why the restrictions on the mutation of overlapping genes aren’t
quite as stringent as you would have the poor people you’re trying to deceive with your
vile lies believe. And now I’m going to proceed to ram those reasons up your jacksie
one by one. One: Just because genes overlap doesn’t
mean that they share exons. The coding sequences of nested or imbedded genes are entirely contained
within one or multiple introns of their hosts, and Makalowska and colleagues showed that
these represent over 50% of overlapping human genes. Since mutations in the imbedded gene
only affect the introns of its host they have no affect on its coding sequence and so aren’t
subject to the restrictions you’re talking about.
Two: The genetic code is redundant. The three nucleotide/four base system produces 64 possible
codons so that, all of the 20 amino acids are represented by more than one. As a result
any given point mutation may be synonymous and result in no change in the protein sequence
in one gene of an overlapping pair, but may concurrently be a missense mutation that alters
the peptide sequence of the other. Three: Not all mis-sense mutations result
in an alteration in protein structure or activity. Such conservative mutations substitute one
amino acid with a structurally similar one which, depending on its structural context
in the protein, may not produce any functional change. This kind of mutation in one gene
may not be so innocuous in the overlapping sibling, allowing the two genes to diverge.
Four: 75% of antisense genes don’t code for protein products and may function to regulate
the transcription of their cognate partners. In this instance mutation of either gene would,
by definition, not be restricted by the other. Five: Gene duplication facilitates the generation
of new copies of the overlapping genes and the subsequent unrestricted generation of
mutant alleles in the present of a functional second copy. I’m not surprised that you
neglected to mention this little tidbit, Neph, because creationists are by now well versed
in deliberately ignoring this well documented and understood process whenever they spuriously
claim that mutation cannot generate “new information.”
And six: Even in the absence of any of these mechanisms you’d still be wrong because
there’s a problem with your argument that’s so big that even someone as astonishingly
simple-minded as ShockofGod will be able to see it. But I’m not going to spill the beans
quite yet Neph, so let’s just let that thought sink and let the tension build a little.
Meanwhile I think I’ll finish on this point, Neph, since you might be feeling rather full.
So while you recovering from the rectal overload let’s watch you frenziedly flogging your
dead horse again as if your friend’s disability check depended on it.
"But the point is that random genetic mutations are degratory to the code of the DNA molecule.
And overlapping and embedded genes is one of the reasons they are so degratory. Because
a random genetic mutation which occurs to one gene very well may effect another…or
another, and another. Or another and another and another."
OK, Neph, I’m not going to bother responding to your deliberately erroneous assertion that
random mutations are “degratory” to the genetic code because that’s already been
roughly stuffed back up your arse more times than your router’s been connected to the
erosguide-dot-com server. Instead I want to focus on the number of times
you used the word “another.” I counted six, so with first gene you mentioned that
makes seven sharing at least one codon. I’ve yet to read of a single report of even a triple-gene
overlap, so I think it’s fair to say that you were being a little less than accurate,
presumably in a transparent attempt to again exaggerate the limitations of gene overlap
on the generation of diversity. The only thing I’m having a hard time with
is distinguishing whether you said this because you were still basking in the afterglow of
a particularly vicious cerebral infraction, or because you’re just a dishonest little
piss-stain who’s willing to say or do anything to maintain his delusion that he actually
has some of argument to make. "Sofia, you’re behind. Genes are indeed
overlapping and embedded. As time goes on we will continue to discover more and more
and more of these overlapping and embedded genes. So far we’ve discovered hundreds.
Before we’re through we may discover many thousands."
As usual, Neph, your assertion is nothing more than a pathetic and easily exposed lie,
though I can’t be sure whether you said it deliberately; or inadvertently because
your head’s permanently wedged up inside your colorectal cavity. So, let’s examine
your claim that we’re only just scratching the surface of the embedded gene count by
taking a little drive down memory lane. Prior to the invention of DNA sequencing it
was thought that one gene coded for just one protein. But following the sequencing of the
first DNA genome, bacteriophage phi X174, by Fred Sanger’s group (a feat which played
a central role in him winning his second Nobel prize), it became clear that there were exceptions
to this rule. Subsequently overlapping genes were discovered
in many viruses and are elegantly explained as an evolutionary strategy to minimize genome
size due to the size restrictions imposed by capsid geometry. Later overlaps were also
found to be relatively common in bacteria, which are also under some evolutionary pressure
to restrict genome size. As an aside, isn’t it interesting, Neph,
that these observations are perfectly understandable in the light of evolutionary theory whereas
your alternative, God did it so he could be dark and mysterious, leaves you as ignorant
as a sad bastard with a pretend degree? Now, getting back on track, it was therefore
surprising that during the late 80’s and 90’s handfuls of overlaps started turning
up in eukaryotes, which were thought to be relatively unaffected by such selective pressures.
Then, following the sequencing of the human and other genomes it became possible to search
for overlaps using algorithms that predict the presence of open reading frames. That’s
where those hundreds you mentioned came from back in 2004 and there’s been no significant
change in the numbers since because there are no more to be found. Your projection of
there being thousands more to come is therefore about as ambitious as Bill Dembski’s and
William Meyer’s hopes for a Nobel prize because, after all, it’s now 2011 now and
we’re still waiting. So with that behind us, we now get to the
point I’ve been looking forward to for the whole of this video, Neph. So tie down on
your headphones, grit your teeth, and hold on tight, because this one’s going to make
your eyes water. "According to this paper thus far are discovered
774 genes overlapping in the human genome, and 542 genes overlapping exons in the human
genome. Compared to 578 genes which are overlapping in the mouse genome, and 455 genes with overlapping
exons in the mouse genome. Notice the difference in the number of overlapping genes. The discovery
of overlapping genes is just in its infancy. As time goes on we continue to discover more
and more genes which are overlapping, or embedded or both."
Of course this last statement only serves to demonstrate that the only thing that’s
in its infancy is your intellectual development, Neph, because I just explained why your claim
about the future trends of overlapping gene discovery is about as accurate as a Kent Hovind
tax return. The mistake you made here was using an actual
paper instead us just showing us your usual series of screen shots of abstracts, laymen’s
science pages and creationist webshites. So the first thing I did was to track down the
actual document and do what you obviously never did, and that’s read it. And having
done that, I’m now in the happy position of being able to use it to beat seven shades
of shit out of you. You see, Neph, while your numbers might sound
impressive to someone who didn’t know any better, you did leave out a minor point. And
that is that these genes were found in genomic databases containing 34,604 human and 33,936
murine genes. Now I’m assuming that long division isn’t
your strong point Neph, so I’ll do the math for you. That means of all the genes examined,
only 2.2% were overlapping in humans and 1.7% in mice. Hardly the impressive figures you
were making them out to be, eh? But wait. It gets better!
Genes that don’t contain exonic overlaps don’t count because mutations in overlapping
introns have no affect on protein sequence and therefore aren’t subject to the mutational
restrictions you’re claiming are a death knell to evolutionary theory.
So when you only count the genes that contain exon overlaps, you come down to values of
1.6% in humans and 1.3% in mice. Not looking any better for you, is it Neph? And if you
think that’s bad then all you have to do is read the rest of the table you showed us
and think back to something I said about exons earlier in this video.
Remember that I said that parts of the exon sequences in the mature mRNA weren’t actually
translated into the protein and therefore weren’t coding? Well it turns out, Neph,
that the vast majority of even these exon overlaps are in non-coding regions. In the
end of the day only 57 human genes overlapped in coding regions and 31 in mice. That’s
works out to be less than 0.1 to 0.2% of all the genes in the human or murine genome Neph,
or as we trained scientists like to put it: absolutely fuck-all.
I’d love to know how you managed to miss all this, Neph. I really would. Was it because
those difficult long words in the paper were just a little too much for you, or because
your chose to ignore it because the truth was just a little too inconvenient for you?
Well, now that I think I’ve unequivocally stuffed your ideas back where they belong,
I should start wrapping up as this has already turned out to be a lot longer than I’d hoped.
And while there were a number of other annoying putrid flecks of misinformation sprinkled
throughout your video, there was one that I felt I just couldn’t let slide. So let’s
take a little look at it and then I’ll let you get off to the pharmacy for a little relief.
"Geneticists today are shying away from the use of the word ‘gene’ because it really
doesn’t properly describe what we observe in the genome of life. The preferred term
is sequences." Do you really believe the mind-bending inanity
of the verbal spew that you bring up every time you open your mouth Neph? That’s a
rhetorical question, of course, because I think it’s quite clear from your videos
that you have a misplaced ego larger than Joel Olsteen’s bank account
Of course this is complete and utter bollocks because the word “sequence” means what
it’s always meant to trained and qualified biological scientists, that is the conceptual
representation of the linear order of bases in any given segment of nucleic acid; while
the word gene refers a unit of heredity that is physically manifested as a specific region
of DNA with a specific sequence. Despite your demented rambling, Neph, nothing’s changed.
Just because an ignorant and intellectually compromised bozo asserts the contrary with
the expectation that his hallucination will be unquestioningly accepted doesn’t change
the definition of these word. It only demonstrates his profound arrogance and the magnitude of
the gulf that separates his perception with that thing that the rest of us refer to as