Are ORFans evidence for design? A provisional analysis

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Ernest Major

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Nov 22, 2006, 11:40:11 AM11/22/06
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Press reports
(<URL:http://www.christianpost.com/article/20061117/23510.htm>) have
recently been brought to our attention, to the effect that Paul Nelson
claims that ORFans are evidence for design.

[Sidebar: ORF is an abbreviation for Open Reading Frame, and refers to a
stretch of DNA inferred from its sequence to code for a protein. An
ORFan is an ORF found in one species for which no ORFs with identifiable
similarities can be found in other species, or in a wider concept of
ORFan similar ORFs can be found only in closely related species. (For a
bacteriologist's concept of closely related - man, mouse, moose and
manatee are closely related by this standard.)

A singleton ORFan has no identifiably similar genes at all; a paralogous
ORFan is a member of a family of genes confined to a single species, and
an orthologous ORFan a member of a family of genes confined a group of
closely related species.]

As I doubt that apologetics reporters are any more accurate than science
reporters I can have no confidence that I know what Paul Nelson claims,
and therefore cannot respond directly to his arguments. However it is
possible to address the evidence independently of the particular
argument that he presented, and I will do so.

In passing I note that the claim in the article "Nearly one-third of the
protein-coding genes of mycoplasma, the simplest “free-living thing”
up until last year, are unknown genes or ORFans. The questions that
result from these discoveries are where did all these genetic
information come from and why are they specific to one bacteria if
according to Darwin’s theory of common descent they have to derive
from a common ancestor?" appears to be factually incorrect. This appears
to be a reference to Mycoplasma genitalium, an obligate parasite, which
has a particularly small genome, and was one of the first organisms to
have its complete genome sequenced. When it was sequenced nearly one
third of its ORFs did not have known homologs in other species. As more
organisms have been sequenced homologs have found, and the current total
of ORFans for M. genitalium is few or none. (This has been known for a
few years [1].) Many of these ORFs are restricted to mycoplasmas, but
not to "one bacteria".

The answer to the question posed in the subject line is in the negative
- even if ORFans were evidence against evolution (common descent) they
not be evidence *for* design; they could equally well have arisen from
Hoylean panspermia.

However, the question as to whether ORFans are evidence against common
descent is worthy of consideration, from two viewpoints. Firstly, it is
likely that they will be presented as such, and it's worth having a
response. Secondly, the theory of evolution has survived a potential
falsification from gene sequence data, but a new opportunity to apply a
potentially falsifying test is arising from the coming availability of
proteome (the set of proteins manufactured by an organism) data.
People ask how evolution is falsifiable sensu Popper. (This presents a
useful answer to those who claim that the theory of evolution is
unfalsifiable and are unimpressed by the many potential falsifying
observations the theory has already survived.)

The theory of evolution predicts that proteomes (the set of proteins
manufactured by an organims) will form a nested hierarchy. It does not
predict that all proteomes will be identical. Proteins can be lost from
proteomes, and new proteins can be formed by duplication and exon
shuffling, and rarely de novo (nylonase). Proteins can diverse so that
they are no longer recognisable as having common ancestry; some protein
families are recognisable only by structure conservation, and not by
sequence conservation.

Note that the theory of evolution predicts that proteomes will form a
nested hierarchy, but does not a priori predict a particular degree of
disparity between proteomes; the latter depends on the age of clades,
and on the rates of sequence change and gene duplication and loss, which
are parameters to be set by observation or experiment. As the degree of
conservation of gene sequences, and the persistence of genes in the
genome, varies between genes we can expect that some proteins will have
broader taxonomic ranges than others.

The particularly potentially falsifying aspect of ORFans is that there
is on current data an excess of ORFans (ORFs found in only a single
species) compared to ORFs of wider taxonomic distribution. The question
which has to be addressed is to what degree that excess is real, and
whether it can accounted for by known processes.

Until we have sequenced sufficient species numbers of ORFans taken from
observation will be overestimates - in some cases the ORF is not a true
ORFan, but we haven't sequenced the genome of any other organism that
shares that ORF. Several studies have compared the genomes of fully
sequenced organisms, but haven't used data from partially sequenced
genomes, and consequently have produced overestimates even by the
standard of the available data. [2]

The majority of false positives (i.e. non-genuine ORFans) can be
eliminated by sequencing closely related species. But a residue may have
arisen by lateral gene transfer, and it may be a long time before the
source is discovered, particularly if it is an unculturable prokaryote.

ORFs of restricted taxonomic distribution, including ORFans, can arise
by several different processes - there isn't a single origin which
applies to all instances.

* Some may be decayed pseudogenes, that is pseudogenes that have
diverged so far from their paralogs that they are unrecognisable. This
has been considered unimportant for bacteria as most bacteria
(Ricksettia and Mycobacterium are exceptions) appear to be efficient at
eliminating pseudogenes.

* Some are of viral origin. The number of this origin appears to be
small, but our current sampling of the diversity of viral proteins is
parse, and the number of ORFans of identified viral origin will be an
underestimate [3]. (As viral genomes don't undergo proofreading they are
less conserved and can diverge to the point of unrecognisability
faster.)

* Some will represent poorly conserved genes.

* Some will result from differential gene loss. A gene may be
insufficiently conserved for its homologs in distant relatives to be
recognised, and lost in all remaining close relatives. (This could
happen, for example, in secondarily non-photosynthetic lineages.)

Summary: ORFans are not evidence for design; it would be premature to
conclude that they are evidence against common descent. (ORFs of erratic
to random taxonomic occurrence would be more problematical than ones of
restricted taxonomic occurrence.) I am reminded of the creationist claim
that GnRH sequences were evidence against common descent - it turned out
that the apparent contradiction was the result of paralogy.

[1] Siew & Fischer, Unravelling the ORFan puzzle, Comp Funct Genom 4:
432–441 (2003)

[2] Mazumder et al, Computational identification of strain-, species-
and genus-specific proteins, BMC Bioinformatics 6: 279 (2005)

[3] Yin & Fischer, On the origin of microbial ORFans: quantifying the
strength of the evidence for viral lateral transfer, BMC Evolutionary
Biology 6: 63 (2006)
--
alias Ernest Major

Gary Bohn

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Nov 22, 2006, 1:26:08 PM11/22/06
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Ernest Major <{$to$}@meden.demon.co.uk> wrote in
news:Q$RfVuHr1...@meden.invalid:

Nominated.

Very good stuff.

--
Gary Bohn

Science rationally modifies a theory to fit evidence, creationism
emotionally modifies evidence to fit a specific interpretation of the
bible.

jgri...@scu.k12.ca.us

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Nov 22, 2006, 1:54:42 PM11/22/06
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> 432-441 (2003)

>
> [2] Mazumder et al, Computational identification of strain-, species-
> and genus-specific proteins, BMC Bioinformatics 6: 279 (2005)
>
> [3] Yin & Fischer, On the origin of microbial ORFans: quantifying the
> strength of the evidence for viral lateral transfer, BMC Evolutionary
> Biology 6: 63 (2006)
> --
> alias Ernest Major

In the article, the premise was... "Darwin said that if there were
systems in nature that could not be arrived at by some gradual means or
process then his theory could be reasonably doubted; the evolution
theory requires gradual steps in biological developments."

Well, the Cambrian Explosion (of life) nullified Darwin's opinion about
exclusively gradual change. The evidence doesn't support Darwin's
concern, since the fossil record contradicts it. And since Evolution is
an adaptive science, no evidence can actually create reasonable doubt.
Darwin's opinion as to what constitutes reasonable doubt must be wrong
(What did he know, anyway?). Any set of facts can be rationalized into
an evolutionary framework. If, exclusively gradual change dictated the
credibility of the Theory of Evolution, then the Cambrian Explosion
would have been ample proof of reasonable doubt.

ORFans are interesting, but if the premise doesn't hold up, they don't
really matter.


JTG 11/22/06

Ernest Major

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Nov 22, 2006, 2:20:26 PM11/22/06
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In message <1164221682.8...@m7g2000cwm.googlegroups.com>,
"jgri...@scu.k12.ca.us" <jgri...@scu.k12.ca.us> writes

I see you're playing a creationist this time.

I hope you're not equivocating on the meaning of the word gradual.
There's no evidence that the Cambrian Explosion is incompatible with
gradual evolution in the sense that Darwin meant, as opposed to a
strawman of evolution occurring at an unvarying rate. You could as well
claim that dog or cabbage breeding falsifies evolution; it seems likely
to me that the rate of morphological change achieved by the breeders
exceed that of the Cambrian Explosion.


>
>ORFans are interesting, but if the premise doesn't hold up, they don't
>really matter.
>
>
>JTG 11/22/06
>

--
alias Ernest Major

John Harshman

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Nov 22, 2006, 3:02:22 PM11/22/06
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jgri...@scu.k12.ca.us wrote:

Nonsense. The Cambrian explosion, depending on how you count it, could
be considered as taking from 5 to 50 million years. Even the lowest
figure is plenty of time for anyone's definition of "gradual".

> The evidence doesn't support Darwin's
> concern, since the fossil record contradicts it.

This is a common error: confusing time as we ordinarily experience it
with geological time. Darwin's "gradual" means small individual steps. A
million years is enough time for a great many small steps to add up to
big steps. The fossil record just isn't fine enough to test this.

> And since Evolution is
> an adaptive science, no evidence can actually create reasonable doubt.
> Darwin's opinion as to what constitutes reasonable doubt must be wrong
> (What did he know, anyway?). Any set of facts can be rationalized into
> an evolutionary framework. If, exclusively gradual change dictated the
> credibility of the Theory of Evolution, then the Cambrian Explosion
> would have been ample proof of reasonable doubt.

Only if you are very confused about time scales. The nihilism here is
yours, not evolutionary biology's

> ORFans are interesting, but if the premise doesn't hold up, they don't
> really matter.

So you think that the only things that matter are those that present
evidence against evolution?

jgri...@scu.k12.ca.us

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Nov 22, 2006, 4:07:37 PM11/22/06
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http://en.wikipedia.org/wiki/Cambrian_explosion

I only know what I read on the internet. Wikipedia specifically
mentions Darwin's reasonable doubt, in light of the Cambrian Explosion.
Unless Wikipedia has been violated by a conspiracy of religious
fundementalists, it's pretty clear that a sudden, not gradual, form of
evolution occurred.

> > The evidence doesn't support Darwin's
> > concern, since the fossil record contradicts it.
>
> This is a common error: confusing time as we ordinarily experience it
> with geological time. Darwin's "gradual" means small individual steps. A
> million years is enough time for a great many small steps to add up to
> big steps. The fossil record just isn't fine enough to test this.

Evolution of the gaps? Lack of evidence as evidence? Can you spell
I-R-O-N-Y? LOL.

>
> > And since Evolution is
> > an adaptive science, no evidence can actually create reasonable doubt.
> > Darwin's opinion as to what constitutes reasonable doubt must be wrong
> > (What did he know, anyway?). Any set of facts can be rationalized into
> > an evolutionary framework. If, exclusively gradual change dictated the
> > credibility of the Theory of Evolution, then the Cambrian Explosion
> > would have been ample proof of reasonable doubt.
>
> Only if you are very confused about time scales. The nihilism here is

> yours, not evolutionary biology's.

Are you finding it hard to accept that evolution could occur rapidly? I
just read a study, where bacteria was evolved over a period of weeks.
That's the sort of thing that's too brief to make the fossil record,
but it doesn't contradict evolution, altogether, unless you accept
Darwin's premise as infallible. We should all be aware of the
fallibility of infallibility.

>
> > ORFans are interesting, but if the premise doesn't hold up, they don't
> > really matter.
>
> So you think that the only things that matter are those that present
> evidence against evolution?

No, the article started with Darwin's premise. If I start with 2 + 2 =
5, it doesn't matter how much I multiply or divide or modify the
variables, I'm starting with something that is false on the face of it.
Darwin was mistaken in his premise, while gradual evolution is the
rule, sudden evolution is the exception. I was of the opinion that this
is universally accepted in our current understanding of Evolution and
at least Wikipedia agrees with my take on it.


JTG later on 11/22/06

Perplexed in Peoria

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Nov 22, 2006, 5:06:00 PM11/22/06
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"Gary Bohn" <gary...@REMOVETHISaccesscomm.ca> wrote in message news:Xns98837E85...@130.133.1.4...

> Ernest Major <{$to$}@meden.demon.co.uk> wrote in
> news:Q$RfVuHr1...@meden.invalid:
>
> > Press reports
> > (<URL:http://www.christianpost.com/article/20061117/23510.htm>) have
> > recently been brought to our attention, to the effect that Paul Nelson
> > claims that ORFans are evidence for design.
> >
[Snip Ernest Major's nice response to Nelson]

> Nominated.
>
> Very good stuff.

Seconded. Though tactically I think we should consider conceding the
issue to Nelson. An intelligent designer is responsible for the mycoplasmas,
but evolution produced everything else. Works for me.

Kermit

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Nov 22, 2006, 5:17:22 PM11/22/06
to

In what way? I believe you badly misunderstand the quote you offer us.
Darwin wasn't saying that evolution had to be slow, in the sense that A
to B must take more than 5,000,000 years. He meant that it had to be in
a sequence of small, simple steps. So a controlling gene might suddenly
add another pair of legs to a centipede ("make ten of these, not
nine"), but it could not, in one fell swoop, add functioning wings to a
horse. No X-men allowed.

The Cambrian Explosion says nothing other than there was a flurry of
activity - a flurry lasting ten million years or so. There is no fossil
(nor other) evidence for hopeful monsters.

> And since Evolution is
> an adaptive science, no evidence can actually create reasonable doubt.

Your conclusion does not follow from your premiss.

Evidence was conceivable which would have made evolutionary theory a
non-starter. For instance, if either of the twiin nested hierarchies
had been missing - morphology or genomes - or if they had not matched,
then evolution would have been seriously questioned or modified.

> Darwin's opinion as to what constitutes reasonable doubt must be wrong
> (What did he know, anyway?). Any set of facts can be rationalized into
> an evolutionary framework.

Nope. If the twin nested hierarchies didn't exist *and match; if the
fossil record did not show a choronological sequence leading from small
and simple to the modern forms; then it would have been impossible to
explain by common descent via modification by natural selection.

> If, exclusively gradual change dictated the
> credibility of the Theory of Evolution, then the Cambrian Explosion
> would have been ample proof of reasonable doubt.

The CE provides no evidence for anything other than incremental
modifications of ancestral forms.

>

> ORFans are interesting, but if the premise doesn't hold up, they don't
> really matter.
>
>
> JTG 11/22/06

Kermit

Ernest Major

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Nov 22, 2006, 6:12:25 PM11/22/06
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In message <cR39h.24728$yl4....@newssvr12.news.prodigy.com>, Perplexed
in Peoria <jimme...@sbcglobal.net> writes

Except that mycoplasmas are not the only organisms with lineage specific
ORFs - Plasmodium falciparum apparently has 60% such. (Until we sequence
another Plasmodium.) It's not clear what level of ORFan genes will be
converged on as we sequence more and more genomes - the current set of
genomes is non-random, which would complicate any attempt to make an
estimate on statistical grounds.
--
alias Ernest Major

Desertphile

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Nov 22, 2006, 6:40:34 PM11/22/06
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jgri...@scu.k12.ca.us wrote:

(Large cut here: please see POTM-worthy material in original)

> In the article, the premise was... "Darwin said that if there were
> systems in nature that could not be arrived at by some gradual means or
> process then his theory could be reasonably doubted; the evolution
> theory requires gradual steps in biological developments."
>
> Well, the Cambrian Explosion (of life) nullified Darwin's opinion about
> exclusively gradual change. The evidence doesn't support Darwin's
> concern, since the fossil record contradicts it. And since Evolution is
> an adaptive science, no evidence can actually create reasonable doubt.
> Darwin's opinion as to what constitutes reasonable doubt must be wrong
> (What did he know, anyway?). Any set of facts can be rationalized into
> an evolutionary framework. If, exclusively gradual change dictated the
> credibility of the Theory of Evolution, then the Cambrian Explosion
> would have been ample proof of reasonable doubt.

Great--- please explain why you believe the Cambrian Explosion was not
gradual.

John Harshman

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Nov 22, 2006, 7:12:29 PM11/22/06
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jgri...@scu.k12.ca.us wrote:

And that's unfortunate.

> Wikipedia specifically
> mentions Darwin's reasonable doubt, in light of the Cambrian Explosion.
> Unless Wikipedia has been violated by a conspiracy of religious
> fundementalists, it's pretty clear that a sudden, not gradual, form of
> evolution occurred.

You need to read the whole article. It's fairly accurate. Darwin was
puzzled by the absence of Pre-Cambrian fossils, but we now know of many,
including the Ediacaran and Doushantuo as well as bilaterian trace
fossils. Darwin also saw the beginning of the Cambrian as the lowest
record of trilobites, and in fact that boundary has been pushed back
quite a bit. The earliest trilobites do not actually appear until 15-20
million years into the Cambrian. The earliest parts of the Cambrian,
before that point, show a gradual increase in the sizes, complexities,
and abundance of both body fossils ("small, shelly fauna") and trace
fossils. No sudden evolution is needed; certainly nothing different from
mutation and selection. As other posters have pointed out, the rates of
natural and artificial selection observed in real time greatly outpace
anything we can estimate from the fossil record.

I could point you to some actual scientific papers if you liked.

>>>The evidence doesn't support Darwin's
>>>concern, since the fossil record contradicts it.
>>
>>This is a common error: confusing time as we ordinarily experience it
>>with geological time. Darwin's "gradual" means small individual steps. A
>>million years is enough time for a great many small steps to add up to
>>big steps. The fossil record just isn't fine enough to test this.
>
> Evolution of the gaps? Lack of evidence as evidence? Can you spell
> I-R-O-N-Y? LOL.

Nothing of the sort. You just have to understand the limitations of data
to distinguish processes. The fossil record can't distinguish between
gradual and sudden evolution at scales less than, say, 100K years.
Resolution for the Cambrian is probably much worse than that. The record
is not evidence for gradual evolution; it's just not evidence against it.

>>>And since Evolution is
>>>an adaptive science, no evidence can actually create reasonable doubt.
>>>Darwin's opinion as to what constitutes reasonable doubt must be wrong
>>>(What did he know, anyway?). Any set of facts can be rationalized into
>>>an evolutionary framework. If, exclusively gradual change dictated the
>>>credibility of the Theory of Evolution, then the Cambrian Explosion
>>>would have been ample proof of reasonable doubt.
>>
>>Only if you are very confused about time scales. The nihilism here is
>>yours, not evolutionary biology's.
>
> Are you finding it hard to accept that evolution could occur rapidly?

Define "rapidly".

> I
> just read a study, where bacteria was evolved over a period of weeks.
> That's the sort of thing that's too brief to make the fossil record,
> but it doesn't contradict evolution, altogether, unless you accept
> Darwin's premise as infallible. We should all be aware of the
> fallibility of infallibility.

How do rapidly evolving bacteria contradict Darwin's premise? I bet
those bacteria evolved by ordinary mutation and selection. True? The
point is that you don't need any extra, magic processes to explain
evolution as rapid as any the fossil record shows.

>>>ORFans are interesting, but if the premise doesn't hold up, they don't
>>>really matter.
>>
>>So you think that the only things that matter are those that present
>>evidence against evolution?
>
> No, the article started with Darwin's premise. If I start with 2 + 2 =
> 5, it doesn't matter how much I multiply or divide or modify the
> variables, I'm starting with something that is false on the face of it.
> Darwin was mistaken in his premise,

So far, nobody has shown any evidence that he was mistaken.

> while gradual evolution is the
> rule, sudden evolution is the exception. I was of the opinion that this
> is universally accepted in our current understanding of Evolution and
> at least Wikipedia agrees with my take on it.

No, Wikipedia doesn't. I can see how a couple of the sentences in that
article, considered in isolation, might be confusing. But you are wrong.
You are confusing time scales here. 5 million years is much longer than
you are capable of imagining. It's longer than I'm capable of imagining
too, but I know to make allowances and so am not confused. Given known
possible rates of evolution by ordinary processes, an incredible amount
of change could fit into that amount of time. Actually, one of the
problems of science is figuring out why sustained rates of morphological
evolution (over millions of years) never come close to being as fast as
what we can observe in the present.

Richard Forrest

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Nov 23, 2006, 7:00:20 AM11/23/06
to

I've just been leafing through my PalAss newsletter, and here is the
abstract for a presentation Nick Butterfield will be giving at the
PalAss conference next month:

"Macroevolution through deep time
Nicholas J, Butterfield
Department of Earth Sciences, University of Cambridge, UK
The fossil record documents two mutually exclusive macroevolutionary
modes separated by the transitional Ediacaran Period. Despite the early
appearance of crown eukaryotes and an oxygenated atmosphere, the
pre-Ediacaran biosphere was populated almost exclusively by microscopic
organisms exhibiting low diversity, no biogeographic partitioning, and
profound morphological/evolutionary stasis. By contrast, the
post-Ediacaran biosphere is characterized by large, diverse organisms,
bioprovinciality and conspicuously dynamic evolution. The difference
can be understood in terms of the unique escalatory co-evolution
accompanying the early Ediacaran introduction of eumetazoans, and their
early Cambrian (Tommotian) radiation into the pelagic realm.
Eumetazoans revolutionized macroecology through their construction of
multi-trophic food webs, which in turn gave rise to large body size,
life history trade-offs, ecological succession, biogeography,
fundamental increases in standing biomass, the invention of
eukaryote-dominated phytoplankton, and the potential for mass
extinction, all of which would have fed back on contemporaneous
biogeochemistry, organismal ecology and macroevolution. Both the
pre-Ediacaran and post-Ediacaran biospheres were inherently stable, but
the former derived from the simplicity of superabundant microbes
exposed to essentially static, physical environments, whereas the
latter is based on eumetazoan-induced diversity and dynamic, biological
environments. The c. 100 million year Ediacaran transition (extending
to the base of the Tommotian) can be defined on evolutionary criteria,
and might usefully be incorporated into the Phanerozoic."

It all makes the Cambrian "explosion" look rather less dramatic than
has been imagined.

RF

Robert Maas, see http://tinyurl.com/uh3t

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Nov 23, 2006, 12:27:54 PM11/23/06
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> From: "jgris...@scu.k12.ca.us" <jgris...@scu.k12.ca.us>

> In the article, the premise was... "Darwin said that if there were
> systems in nature that could not be arrived at by some gradual means or
> process then his theory could be reasonably doubted; the evolution
> theory requires gradual steps in biological developments."

Note such a case would only cause the theory to be doubted, not
rejected. We expect a vast majority of viable mutations to be tiny
changes, but an occasional one to be some gross rearrangement of
existing parts that happens to *also* work (although most likely
for a completely different function). Darwin didn't know that a
sequence of nucleic acid bases determines the genome, so he had no
way to know there'd be frequent point mutations and occasional
gross rearrangements. We have that extra information as to the
underlying mechanism of heredity, so we might use the same words he
used but de-emphasize the word "doubt" and include a qualifier
where there'd have to be lots of such systems to be any real
problem. And we have lots of statistical evidence showing indeed
lots of minor mutations and just a few major rearrangements, so we
have no reasonable doubt about evolutionary theory being basically
true.

> Well, the Cambrian Explosion (of life) nullified Darwin's opinion
> about exclusively gradual change.

I'm not aware of even one system that came into being during the
"Cambrian Explosion" and which has been proved couldn't have
evolved via gradual change (meaning lots of little mutations, *not*
meaning an actual continuous change). What most likely happened
during the C.E. was that some species happened to discover a way to
make hard body parts, either for protection from preditors or
within a preditor to kill and grind the prey, and then horizontal
gene flow allowed other species to acquire similar capability,
causing an "arms race".

> Any set of facts can be rationalized into an evolutionary
> framework.

Not true. Any evolutionary framework restricts events to new things
based on variations of old things. For example, wings are
variations on forelimbs which are variations on fins. Wings don't
suddenly appear fully formed in places where there were no limbs in
the first place, such as in the myth of "angels" which are shaped
just like humans but with wings added. At the biochemical level,
evidence of each species having a totally different genetic code or
totally different enzymes would cause a problem with evolution. In
fact we see no such thing. Minor variations in the genetic code
occur only in very divergent clades, including the endosymbionts
(nucleus, mitochondria, plastid) in eukaryotes, not between
individuals in tiny recent clades. Enzymes vary more, but still
vary only a little bit within small clades and a bit more between
small clades within larger clades, and *some* enzymes and
biochemical pathways vary seriously between the major clades.

> If, exclusively gradual change dictated the credibility of the
> Theory of Evolution, then the Cambrian Explosion would have been
> ample proof of reasonable doubt.

Nope, both your minor premise (C.E. shows example of non-gradual
change) and your major premise (single example of non-gradual
change refutes evolutionary theory) are false. Per Darwin's
original understanding, your major premise might have been true,
but that's irrelevant to the question of whether current
evolutionary theory is supported by evidence or not. Darwin was
wrong about a few points, but his basic idea was correct and the
detailed theory has been augmented and fixed per those few points
to be more correct than the original. By comparison, both the
Biblical idea and Lamarck's idea have been shown almost totally
mistaken, not a valid basis for any workable theory.

And don't forget Wallace! He came up with the same idea as Darwin
independently at about the same time. Does anybody know of an
online review comparing their two presentations, in particular any
significant differences in their theories? I'm mildly curious, at
the moment, in the context of this thread, where either of their
two versions needed more fixups than the other to arrive at
present-day evolutionary theory.

As to the main topic of this thread, ORFans: I expect that whenever
there's a tight modern clade of different species, virtually all
the DNA will be alignable between the different species, including
what were formerly thought of as ORFans. But in cases where there's
only a single modern species with a deep branch since the LCA with
any other species, there might be some ORFans in that isolated
species which can't be aligned with any other species. Let's see if
my prediction turns out to be correct in a decade or two after
we've fully sequenced tens of millions of species/strains.

david ford

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Nov 24, 2006, 7:51:05 AM11/24/06
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"evolution produced everything else"

Meaning of "evolution"?
http://groups.google.com/groups?selm=dford3-386md9F5lsv5cU1%40individual.net

How do you account for the origination of ORFans?

2006
http://www.biomedcentral.com/1471-2148/6/63
The origin of microbial ORFans, ORFs having no
detectable homology to other ORFs in the
databases, is one of the unexplained puzzles of the
post-genomic era.

CreateThis

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Nov 24, 2006, 12:23:12 PM11/24/06
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On 24 Nov 2006 04:51:05 -0800, "david ford" <dfo...@gl.umbc.edu>
wrote:

Hey! Back in your box!

<re-plonk>

CT

Hollis Brown

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Nov 24, 2006, 12:40:28 PM11/24/06
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NNTP-Posting-Host: darwin

david ford

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Nov 24, 2006, 1:52:14 PM11/24/06
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CreateThis wrote:

david ford

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Nov 24, 2006, 2:02:14 PM11/24/06
to
Gary Bohn wrote:
> Ernest Major <{$to$}@meden.demon.co.uk> wrote in
> news:Q$RfVuHr1...@meden.invalid:
>
> Nominated.
>
> Very good stuff.

A table at
http://www.cs.bgu.ac.il/~nomsiew/ORFans/genomes.html

lists large #s/ "no. of ORFs." How do you account for
the origination of ORFans?

////////////////////////////////////////////////////////////////////////////////////////////////

david ford

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Nov 24, 2006, 2:35:26 PM11/24/06
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Richard Forrest wrote in "Re: Are ORFans evidence for design? A
provisional analysis":

[snip]

"we identify 382 of the 482 M. genitalium protein-coding genes as
essential"

Dr Forrest, how does atheism account for the origination of those 382
essential genes?

"Genes encoding proteins of unknown function constitute 28% of the
essential protein-coding genes set."

Biologists, what are the functions of those genes?

Glass, John I., et al. 10 January 2006. "Essential genes of a minimal
bacterium" _Proceedings of the National Academy of Sciences USA_ 103:
425-430. The abstract, from
http://www.pnas.org/cgi/content/full/103/2/425
Mycoplasma genitalium has the smallest genome of
any organism that can be grown in pure culture. It
has a minimal metabolism and little genomic
redundancy. Consequently, its genome is expected
to be a close approximation to the minimal set of
genes needed to sustain bacterial life. Using global
transposon mutagenesis, we isolated and
characterized gene disruption mutants for 100
different nonessential protein-coding genes. None
of the 43 RNA-coding genes were disrupted.

Herein, we identify 382 of the 482 M. genitalium
protein-coding genes as essential, plus five sets of
disrupted genes that encode proteins with
potentially redundant essential functions, such as
phosphate transport. Genes encoding proteins of
unknown function constitute 28% of the essential
protein-coding genes set. Disruption of some genes
accelerated M. genitalium growth.

How does atheism account for the origination of the "about 100 genes of
unknown function" referred to below?

Hutchison III, Clyde A., et al. 1999. "Global Transposon Mutagenesis
and a Minimal Mycoplasma Genome" _Science_ 286: 2165-2169. The
abstract, from
http://www.sciencemag.org/cgi/content/abstract/286/5447/2165?ijkey=4ffdcc413fc0ef90524c454ef65bc5291ed451e8&keytype2=tf_ipsecsha
Mycoplasma genitalium with 517 genes has the
smallest gene complement of any independently
replicating cell so far identified. Global transposon
mutagenesis was used to identify nonessential
genes in an effort to learn whether the naturally
occurring gene complement is a true minimal
genome under laboratory growth conditions. The
positions of 2209 transposon insertions in the

completely sequenced genomes of M. genitalium
and its close relative M. pneumoniae were
determined by sequencing across the junction of the
transposon and the genomic DNA. These junctions
defined 1354 distinct sites of insertion that were not
lethal. The analysis suggests that 265 to 350 of the
480 protein-coding genes of M. genitalium are
essential under laboratory growth conditions,
including about 100 genes of unknown function.

///////////////////////////////////////////////////////////////////////////////////////////////////
1985 Cairns-Smith: "Present-day organisms are manifestly pieces of
'high technology', and what is more seem to be necessarily so."
http://groups.google.com/groups?selm=dford3-1123558517.582123.223890%40o13g2000cwo.googlegroups.com

1985 A.G. Cairns-Smith; How did recorded-in-DNA/ genetic information
originate?
http://groups.google.com/groups?selm=dford3-32gv43F3jsrelU1%40individual.net

How does a seeingwatchmakingist account for the origin of
the recorded-in-DNA/ genetic information within:
a human? a bacterium? the first biological lifeform?
http://groups.google.com/groups?selm=dford3-348nj6F47evohU1%40individual.net

david ford

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Nov 24, 2006, 2:49:44 PM11/24/06
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John Harshman wrote:
> jgri...@scu.k12.ca.us wrote:
> > Well, the Cambrian Explosion (of life) nullified Darwin's opinion about
> > exclusively gradual change.
>
> Nonsense. The Cambrian explosion, depending on how you count it, could
> be considered as taking from 5 to 50 million years. Even the lowest
> figure is plenty of time for anyone's definition of "gradual".

"The Cambrian explosion... could be considered as taking


from 5 to 50 million years."

How so? Details, please.

From: "david ford" <dfo...@gl.umbc.edu>
Newsgroups: talk.origins,alt.atheism,alt.talk.creationism,talk.atheism
Subject: timeframe of Cambrian explosion?
Date: 21 Sep 2006 08:53:08 -0700
Lines: 77
Message-ID:
<dford3-11588539...@i42g2000cwa.googlegroups.com>

Over what timeframe, and during what years, did the 'Cambrian
explosion'-- biology's big bang-- occur?

Did the Cambrian explosion occur during 530-525 million years ago?

Did the Cambrian explosion occur during a timeframe of at-most 10
million years?

///////////////////////////////////////////////////////////////////////////////////////////////
Nash, J. Madeleine. 4 December 1995. "When Life Exploded"
_TIME Magazine_, 66-74. Some pics from the article are at
http://www.usc.edu/dept/mda/180evolution/IMAGES/wle.html
On 70, text from
http://www.time.com/time/magazine/printout/0,8816,983789,00.html
Evolving at Supersonic Speed
SCIENTISTS USED TO THINK THAT THE
EVOlution of phyla took place over a period of 75
million years, and even that seemed impossibly
short. Then two years ago, a group of researchers
led by Grotzinger, Samuel Bowring from M.I.T. and
Harvard's Knoll took this long-standing problem and
escalated it into a crisis. First they recalibrated the
geological clock, chopping the Cambrian period to
about half its former length. Then they announced
that the interval of major evolutionary innovation did
not span the entire 30 million years, but rather was
concentrated in the first third. "Fast," Harvard's
Gould observes, "is now a lot faster than we
thought, and that's extraordinarily interesting."
==
Zircon dating, which calculates a fossil's age by
measuring the relative amounts of uranium and lead
within the crystals, had been whittling away at the
Cambrian for some time.
==
Now, with information based on the lead content of
zircons from Siberia, virtually everyone agrees that
the Cambrian started almost exactly 543 million
years ago and, even more startling, that all but one
of the phyla in the fossil record appeared within the
first 5 million to 10 million years. "We now know how
fast fast is," grins Bowring. "And what I like to ask
my biologist friends is, How fast can evolution get
before they start feeling uncomfortable?"

June 2006
Ann Coulter's "Flatulent Raccoon Theory"
by Robert Savillo of Media Matters for America
http://mediamatters.org/items/200607070010
Among her falsehoods, misinformation, and
distortions, Coulter:
==
* Distorts the duration of the period known as the
Cambrian explosion, omits important information
about its significance, and suggests that 10 million
years is "sudden."
==
Coulter also distorts other aspects of the Cambrian
period. On Page 221, she claims, "The best
estimate for the duration of the Cambrian explosion
is [...] 5 to 10 million years. And that is the maximum
length."
==
On the previous page, Coulter also distorts the
Cambrian explosion, describing the event as "a
period of less than 10 million years" and "a sudden
explosion of nearly all the animal phyla we have
today." While 5 to 10 million years is within the
range of estimates for the duration of the Cambrian
explosion, it is by no means "the maximum length"
according to scientists. Additionally, even 5 million
years-- the shortest estimate-- is hardly "sudden."

Explosion of Life: A scientist [Paul Chien] reveals details of the
Cambrian explosion
http://www.origins.org/articles/chien_explosionoflife.html

> > The evidence doesn't support Darwin's
> > concern, since the fossil record contradicts it.
>
> This is a common error: confusing time as we ordinarily experience it
> with geological time. Darwin's "gradual" means small individual steps. A
> million years is enough time for a great many small steps to add up to
> big steps. The fossil record just isn't fine enough to test this.

"Darwin's 'gradual' means small individual steps."

"a great many small steps... add up to big steps"

_Paleobiology_ 3: 134 (1977), Gould & Eldredge:
In fact, most published commentary on punctuated equilibria has
been favorable. We are especially pleased that several
paleontologists now state with pride and biological confidence
a conclusion that had previously been simply embarrassing ('all
these years of work and I haven't found any evolution').

Essay on Problems with Darwin's Theory of Natural Selection
http://groups.google.com/groups?selm=Pine.LNX.4.10A.B3.10005310900310.17702-100000%40jabba.gl.umbc.edu

> > And since Evolution is
> > an adaptive science, no evidence can actually create reasonable doubt.
> > Darwin's opinion as to what constitutes reasonable doubt must be wrong
> > (What did he know, anyway?).

Dawkins, Richard. 1989. _The Selfish Gene_ (Oxford: Oxford
University Press), 352pp., 195:
Much of what Darwin said is, in detail, wrong.
surrounding material in
http://groups.google.com/groups?selm=u2k2i0dlm2htnq42avhemsueaqi7pje2mh%404ax.com

> > Any set of facts can be rationalized into
> > an evolutionary framework.

ReMine, and Birch & Ehrlich on the unfalsifiability of the ToE
http://groups.google.com/groups?selm=Pine.SGI.3.96A.990620062330.18490880A-100000%40umbc9.umbc.edu

ID as a metaphysical research program
http://groups.google.com/groups?selm=dford3-1129317540.779352.231140%40f14g2000cwb.googlegroups.com

> > If, exclusively gradual change dictated the
> > credibility of the Theory of Evolution, then the Cambrian Explosion
> > would have been ample proof of reasonable doubt.
>
> Only if you are very confused about time scales. The nihilism here is
> yours, not evolutionary biology's
>
> > ORFans are interesting, but if the premise doesn't hold up, they don't
> > really matter.
>
> So you think that the only things that matter are those that present
> evidence against evolution?

Meaning of [JH]"evolution"?
http://groups.google.com/groups?selm=dford3-386md9F5lsv5cU1%40individual.net

Mark Isaak

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Nov 24, 2006, 3:46:27 PM11/24/06
to
On Wed, 22 Nov 2006 18:26:08 +0000, Gary Bohn wrote:

> Ernest Major <{$to$}@meden.demon.co.uk> wrote in
> news:Q$RfVuHr1...@meden.invalid:
>
>> Press reports
>> (<URL:http://www.christianpost.com/article/20061117/23510.htm>) have
>> recently been brought to our attention, to the effect that Paul Nelson
>> claims that ORFans are evidence for design.
>>

>> [...]
>
> Nominated.

Seconded.

--
Mark Isaak eciton (at) earthlink (dot) net
"Voice or no voice, the people can always be brought to the bidding of
the leaders. That is easy. All you have to do is tell them they are
being attacked, and denounce the pacifists for lack of patriotism and
exposing the country to danger." -- Hermann Goering

Ron Baker, Pluralitas!

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Nov 24, 2006, 4:22:00 PM11/24/06
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"david ford" <dfo...@gl.umbc.edu> wrote in message
news:dford3-11643969...@j72g2000cwa.googlegroups.com...

Trolling.

Glenn

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Nov 24, 2006, 4:54:19 PM11/24/06
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That's not true, for anyone. 6 million or more years to evolve two
primates that appear almost identical, and 50 million years to go from
virtually a single cell to a fish, doesn't match up any where close.
That's why there are these theories of catastrophic events, cosmic ray
storms, oxygen increase, etc. increasing this "gradualness" most
significantly.


>
> > The evidence doesn't support Darwin's
> > concern, since the fossil record contradicts it.
>
> This is a common error: confusing time as we ordinarily experience it
> with geological time. Darwin's "gradual" means small individual steps. A
> million years is enough time for a great many small steps to add up to
> big steps. The fossil record just isn't fine enough to test this.

This has always seemed to me to be one of the best excuses
evolutionists have ever devised. All the while claiming that the fossil
record is sufficient to "test this" and eveything else to boot. It is
much more likely (parsimonious), that many more intemediates would be
found to evidence small graduations, as they are in what is found to
evidence graduations on a larger scale. Perhaps exponentially more
likely in general, since unless there are hopeful monsters, there
*would* be many many more fossils that show fine graduations, than
finding only a few "intermediates" purporting to show large changes.
You haven't got lucky, John, and you can't use luck as an argument.
Either there is an adequate number of fossils or there is not. Be real.
You can't just claim there is because you think you can claim that what
has been found supports your theory.
>
snip

Glenn

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Nov 24, 2006, 5:08:40 PM11/24/06
to

Thanks, David. At least someone is willing to actually post a real, and
accessible reference on this, instead of relying on lips flapping in
the wind.

Glenn

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Nov 24, 2006, 5:07:37 PM11/24/06
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Thanks, David. At least someone is willing to actually post a real, and

Ernest Major

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Nov 24, 2006, 5:32:16 PM11/24/06
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In message <1164406057.1...@f16g2000cwb.googlegroups.com>,
Glenn <GlennS...@msn.com> writes
Your attention span is nearly as bad as Mr. Ford's. That same reference
(OK, sans URL) was given at the top of the thread.
--
alias Ernest Major

Perplexed in Peoria

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Nov 24, 2006, 5:37:49 PM11/24/06
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"david ford" <dfo...@gl.umbc.edu> wrote in message news:dford3-11643969...@j72g2000cwa.googlegroups.com...

How does creation by a benevolent God account for this organism's creation?
What role does it play in the divine plan?

As I understand it, there is also an ORFan problem with Plasmodium falciparum.
The so-called 'falcip' strain of malaria was considered a serious problem
back in the Vietnam war days, because it didn't respond well to the usual
anti-malarial drugs. Why did God create this organism?

I'm really puzzled as to how this ORFan business can be considered evidence
for the Hand of God in creation.

Glenn

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Nov 24, 2006, 5:45:05 PM11/24/06
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And you say there is something wrong with my attention *span*?? How
much of your attention was "spanned" from my post to yours, dude? I
said accessible. Your references are not real until I looked them up
and read them, if they existed or held what you claimed they held at
all. They were not real in the sense that references aren't necessarily
real, but only words requiring verification. You've just stepped up and
put new meaning to the expression lips flapping in the wind.

Perplexed in Peoria

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Nov 24, 2006, 6:12:53 PM11/24/06
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"Perplexed in Peoria" <jimme...@sbcglobal.net> wrote in message news:1vK9h.9773$yE6....@newssvr14.news.prodigy.com...

>
> "david ford" <dfo...@gl.umbc.edu> wrote in message news:dford3-11643969...@j72g2000cwa.googlegroups.com...
> > Richard Forrest wrote in "Re: Are ORFans evidence for design? A
> > provisional analysis":
> >
> > [snip]
> >
> > "we identify 382 of the 482 M. genitalium protein-coding genes as
> > essential"
> >
> > Dr Forrest, how does atheism account for the origination of those 382
> > essential genes?
> >
> > "Genes encoding proteins of unknown function constitute 28% of the
> > essential protein-coding genes set."
> >
> > Biologists, what are the functions of those genes?

Theists, what are the functions of these organisms? I have a pretty
good idea what approaches biologists will take to discover the answer
to your question. Pretty much the same approaches that have proved so
successful in discovering the functions of every other gene. But I
am truly Perplexed as to what the research strategy of the Discovery
Institute will be as they try to answer my question. They are planning
to do that research, right?

Uncle Vic

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Nov 24, 2006, 7:37:54 PM11/24/06
to
Once upon a time in alt.atheism, dear sweet david ford (dford3
@gl.umbc.edu) made the light shine upon us with this:

> can atheism account for origination of 382 essential genes?

Atheism is the lack of belief in gods. That's all.


--
Uncle Vic
aa Atheist #2011
Supervisor, EAC Department of little adhesive-backed "L" shaped
chrome-plastic doo-dads to add feet to Jesus fish department.
Proud member of Earthquack's "Ghost fulla holes" convict page

Glenn

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Nov 24, 2006, 7:54:45 PM11/24/06
to

Uncle Vic wrote:
> Once upon a time in alt.atheism, dear sweet david ford (dford3
> @gl.umbc.edu) made the light shine upon us with this:
>
> > can atheism account for origination of 382 essential genes?
>
> Atheism is the lack of belief in gods. That's all.
>
You are very alone in that assumption.

Dr.GH

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Nov 24, 2006, 7:59:42 PM11/24/06
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"can atheism account for origination of 382 essential genes?"

Stupid question! Oh! It is David Ford.

No wonder.

Free Lunch

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Nov 24, 2006, 8:02:56 PM11/24/06
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On 24 Nov 2006 16:54:45 -0800, in talk.origins
"Glenn" <GlennS...@msn.com> wrote in
<1164416085.3...@j44g2000cwa.googlegroups.com>:

Hardly.

Why do you claim it means something else? It certainly has nothing to do
with science.

Glenn

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Nov 24, 2006, 8:06:40 PM11/24/06
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How'd you figure that?

Glenn

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Nov 24, 2006, 8:12:58 PM11/24/06
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Free Lunch wrote:
> On 24 Nov 2006 16:54:45 -0800, in talk.origins
> "Glenn" <GlennS...@msn.com> wrote in
> <1164416085.3...@j44g2000cwa.googlegroups.com>:
> >
> >Uncle Vic wrote:
> >> Once upon a time in alt.atheism, dear sweet david ford (dford3
> >> @gl.umbc.edu) made the light shine upon us with this:
> >>
> >> > can atheism account for origination of 382 essential genes?
> >>
> >> Atheism is the lack of belief in gods. That's all.
> >>
> >You are very alone in that assumption.
>
> Hardly.

No, not hardly. Vey alone.


>
> Why do you claim it means something else? It certainly has nothing to do
> with science.

Neither did the question use the word science, nor did I say it "meant
something else". A lack of belief is not all atheism is. Atheism is
also a belief that there is evidence against the existence of God.
Personally, I think atheism (and you enforce this) is similar to a
lobotomy gone terribly wrong.

Free Lunch

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Nov 24, 2006, 8:22:41 PM11/24/06
to
On 24 Nov 2006 17:12:58 -0800, in talk.origins
"Glenn" <GlennS...@msn.com> wrote in
<1164417178.5...@l39g2000cwd.googlegroups.com>:

>
>Free Lunch wrote:
>> On 24 Nov 2006 16:54:45 -0800, in talk.origins
>> "Glenn" <GlennS...@msn.com> wrote in
>> <1164416085.3...@j44g2000cwa.googlegroups.com>:
>> >
>> >Uncle Vic wrote:
>> >> Once upon a time in alt.atheism, dear sweet david ford (dford3
>> >> @gl.umbc.edu) made the light shine upon us with this:
>> >>
>> >> > can atheism account for origination of 382 essential genes?
>> >>
>> >> Atheism is the lack of belief in gods. That's all.
>> >>
>> >You are very alone in that assumption.
>>
>> Hardly.
>
>No, not hardly. Vey alone.

Atheism is the lack of belief in gods. Full stop. You may feel the
desire to redefine the word to fit your religiously inspired bigotry,
but that won't make it true.

>> Why do you claim it means something else? It certainly has nothing to do
>> with science.
>
>Neither did the question use the word science, nor did I say it "meant
>something else". A lack of belief is not all atheism is. Atheism is
>also a belief that there is evidence against the existence of God.

Some may have that belief, some may not. It is certainly not necessary
to conclude that there is evidence against gods to be an atheist.

>Personally, I think atheism (and you enforce this) is similar to a
>lobotomy gone terribly wrong.

Would you know about that from personal experience?

--

"... There's glory for you."

"I don't know what you mean by 'glory,'" Alice said.

Humpty Dumpty smiles contemptuously. "Of course you don't--till
I tell you. I meant 'there's a nice knock-down argument for you!'"

"But glory doesn't mean "a nice knock-down argument," Alice objected.

"When I use a word," Humpty Dumpty said, in a rather scornful tone,
"it means just what I choose it to mean--neither more nor less."

"The question is," said Alice "whether you can make words mean so
many different things."

"The question is," said Humpty Dumpty, "which is to be master--that's
all."

Peter Barber

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Nov 24, 2006, 8:34:35 PM11/24/06
to

<pantomime>Ooohhhh, no, he's not!</pantomime>

Peter Barber

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Nov 24, 2006, 8:54:12 PM11/24/06
to

Granted that absence of evidence for X ≠ evidence of absence of X,
but that is simply an admonition not to jump to conclusions in the
absence of evidence. It is most certainly not an argument in favour of
the existence of X by default. And as we collect more and more evidence
about the natural world without detecting traces of a deity's
involvement, the more reasonable it becomes to conclude that no deity
exists.

Since we're talking about definitions of words, may I suggest replacing
'enforce' with 'reinforce'? i.e. You think that atheism is similar to a
lobotomy gone terribly wrong, and Free Lunch *reinforces* this
[impression].

And yes, apparently the lobotomy *did* go wrong - it destroyed the
nucleus religiosus instead of part of the frontal cortex. I understand
that Free Lunch decided not to sue the hospital, having considered the
outcome :-D


Glenn

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Nov 24, 2006, 9:07:00 PM11/24/06
to

Like I said, a lobotomy gone terribly wrong.


>
> Since we're talking about definitions of words, may I suggest replacing
> 'enforce' with 'reinforce'? i.e. You think that atheism is similar to a
> lobotomy gone terribly wrong, and Free Lunch *reinforces* this
> [impression].

Yes, you may. Learning new words is always helpful LOL! I recall that I
was going to say "further support", then thought instead of support, to
use enforce, and left out the "re". Sue me.


>
> And yes, apparently the lobotomy *did* go wrong - it destroyed the
> nucleus religiosus instead of part of the frontal cortex. I understand
> that Free Lunch decided not to sue the hospital, having considered the
> outcome :-D

It doesn't seem to have helped him, by the look of his last post. It
sure doesn't look like it helped you. Your original equation didn't
happen to include "reasonable", dude. I suggest another operation to
remove the rest of the affected areas.


Von R. Smith

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Nov 24, 2006, 9:10:42 PM11/24/06
to

Glenn wrote:
> Free Lunch wrote:
> > On 24 Nov 2006 16:54:45 -0800, in talk.origins
> > "Glenn" <GlennS...@msn.com> wrote in
> > <1164416085.3...@j44g2000cwa.googlegroups.com>:
> > >
> > >Uncle Vic wrote:
> > >> Once upon a time in alt.atheism, dear sweet david ford (dford3
> > >> @gl.umbc.edu) made the light shine upon us with this:
> > >>

<snip>


> Personally, I think atheism (and you enforce this) is similar to a
> lobotomy gone terribly wrong.


Whereas fundamentalism is similar to one that succeeded?

Mark K. Bilbo

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Nov 24, 2006, 10:20:20 PM11/24/06
to
On Fri, 24 Nov 2006 10:52:14 -0800, david ford wrote:

> CreateThis wrote:
>> On 24 Nov 2006 david ford <dfo...@gl.umbc.edu> wrote:
>>
>> Hey! Back in your box!
>>
>> <re-plonk>
>
> How do you account for the origination of ORFans?

Oh lookie, Fnord found a new toy!

--
Mark K. Bilbo
------------------------------------------------------------
"Christians, it is needless to say, utterly detest each other.
They slander each other constantly with the vilest forms of
abuse and cannot come to any sort of agreement in their
teachings. Each sect brands its own, fills the head of its
own with deceitful nonsense, and makes perfect little pigs
of those it wins over to its side." -Celsus (2nd century C.E.)

Peter Barber

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Nov 24, 2006, 11:38:08 PM11/24/06
to

Leave out the silly non sequiturs, please. Let's try again: Assume you
want to work out if God (here used to denote any supernatural being)
exists.

Before the age of scientific research, it wasn't possible to infer from
the lack of evidence for God that God does not exist. However, despite
the collection of a phenomenal amount of data about the natural world
by scientists over the last two centuries, no evidence has surfaced of
the arbitrary suspension of physical laws (a.k.a. miracles) which would
suggest the intervention of God. The more data that is collected
without turning up such evidence, the less likely it becomes that God
exists. At this point in time I would argue that the probability of
God's existence is now so small as to be negligible.

Is that more clear?

> > Since we're talking about definitions of words, may I suggest replacing
> > 'enforce' with 'reinforce'? i.e. You think that atheism is similar to a
> > lobotomy gone terribly wrong, and Free Lunch *reinforces* this
> > [impression].
>
> Yes, you may. Learning new words is always helpful LOL! I recall that I
> was going to say "further support", then thought instead of support, to
> use enforce, and left out the "re". Sue me.
>
> > And yes, apparently the lobotomy *did* go wrong - it destroyed the
> > nucleus religiosus instead of part of the frontal cortex. I understand
> > that Free Lunch decided not to sue the hospital, having considered the
> > outcome :-D
>
> It doesn't seem to have helped him, by the look of his last post. It
> sure doesn't look like it helped you. Your original equation didn't
> happen to include "reasonable", dude.

Please explain this.

> I suggest another operation to
> remove the rest of the affected areas.

No, thanks. It seems I was born without a tendency to religious belief,
so there's nothing that needs removal.


bob young

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Nov 25, 2006, 12:36:02 AM11/25/06
to

johac

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Nov 25, 2006, 1:34:24 AM11/25/06
to
In article
<dford3-11643969...@j72g2000cwa.googlegroups.com>,
"david ford" <dfo...@gl.umbc.edu> wrote:

> Richard Forrest wrote in "Re: Are ORFans evidence for design? A
> provisional analysis":
>
> [snip]
>
> "we identify 382 of the 482 M. genitalium protein-coding genes as
> essential"
>
> Dr Forrest, how does atheism account for the origination of those 382
> essential genes?
>

3.5 billion years of evolution.
--
John Hachmann aa #1782

"Those who can make you believe absurdities can make you commit atrocities"
-Voltaire

Contact - Throw a .net over the .com

rev.goetz

unread,
Nov 25, 2006, 3:22:52 AM11/25/06
to

Ernest Major wrote:
> Press reports
> (<URL:http://www.christianpost.com/article/20061117/23510.htm>) have
> recently been brought to our attention, to the effect that Paul Nelson
> claims that ORFans are evidence for design.
>

All ORFans are tentative ORFans till we sequence every extant genome.
And even if that would happen, we would still be missing the genomic
data from the majority of species that existed.

Dr.GH

unread,
Nov 25, 2006, 3:26:28 AM11/25/06
to

In what way is atheism, or theism challenged or supported?

If we find the specific pathways for the evolution of 300, or 30,000
genes a thiest can simply say that that was the wat their deity of
choice "menat it to be." On the other side, there is no reason that an
evolutionary theory or model needs to account for the exact base by
base sequence of any gene, regardless of Mike Behe's fatuous demand.

Can you tell me the exact trajectory of every bullet fired in World War
II? If you can't, why do you think the war happened? How can you tell
who won?

The question is stupid because it cannot be used to distinguish
anything.

ErikW

unread,
Nov 25, 2006, 6:17:26 AM11/25/06
to

It would expect that most complete bacterial genomes are host
associated (i.e.human pathogens) and not free living. Parasites often
have small genomes since it can use the host for a bunch of things and
the same logic should apply to pathogens. I'd expect lots of sequence
"decay" and deletions in non-used genes just from this alone and I
think that the (potential) bias towards pathogens could be a
substantial source of ORFans in the currently available genomes. A
prediction would be that pathogens have more non-functional ORFans than
free living bacteria. FWIW.

Thanks for a good post.

ErikW

Ernest Major

unread,
Nov 25, 2006, 7:52:44 AM11/25/06
to
In message <1164453446....@h54g2000cwb.googlegroups.com>, ErikW
<bryo...@hotmail.com> writes

>> * Some will result from differential gene loss. A gene may be
>> insufficiently conserved for its homologs in distant relatives to be
>> recognised, and lost in all remaining close relatives. (This could
>> happen, for example, in secondarily non-photosynthetic lineages.)
>
>It would expect that most complete bacterial genomes are host
>associated (i.e.human pathogens) and not free living. Parasites often
>have small genomes since it can use the host for a bunch of things and
>the same logic should apply to pathogens. I'd expect lots of sequence
>"decay" and deletions in non-used genes just from this alone and I
>think that the (potential) bias towards pathogens could be a
>substantial source of ORFans in the currently available genomes. A
>prediction would be that pathogens have more non-functional ORFans than
>free living bacteria. FWIW.

That doesn't seem to be the explanation for ORFans in bacteria in
general, on two grounds, though the prediction on the relative numbers
of non-functional ORFans may be valid. Firstly bacteria lose unused
genes rapidly in evolutionary time, and secondly many bacterial ORFans
have been demonstrated to be not only functional but essential (in that
organism).

On the other hand, parasites, in addition to their tendency to genome
reduction, also show a tendency to more rapid sequence evolution. Hence
a bias towards pathogens could introduce a bias towards organisms with
highly divergent (unrecognisable) sequences, and an overestimate of the
typical proportion of ORFans in genomes.
--
alias Ernest Major

Richard Forrest

unread,
Nov 25, 2006, 8:16:00 AM11/25/06
to

david ford wrote:
> Richard Forrest wrote in "Re: Are ORFans evidence for design? A
> provisional analysis":
>
> [snip]
>
> "we identify 382 of the 482 M. genitalium protein-coding genes as
> essential"
>
> Dr Forrest, how does atheism account for the origination of those 382
> essential genes?

It doesn't.

Your point?

Oh, sorry: you never have one.

RF

>
> "Genes encoding proteins of unknown function constitute 28% of the
> essential protein-coding genes set."
>
> Biologists, what are the functions of those genes?
>

> Glass, John I., et al. 10 January 2006. "Essential genes of a minimal
> bacterium" _Proceedings of the National Academy of Sciences USA_ 103:
> 425-430. The abstract, from
> http://www.pnas.org/cgi/content/full/103/2/425
> Mycoplasma genitalium has the smallest genome of
> any organism that can be grown in pure culture. It
> has a minimal metabolism and little genomic
> redundancy. Consequently, its genome is expected
> to be a close approximation to the minimal set of
> genes needed to sustain bacterial life. Using global
> transposon mutagenesis, we isolated and
> characterized gene disruption mutants for 100
> different nonessential protein-coding genes. None
> of the 43 RNA-coding genes were disrupted.
>
> Herein, we identify 382 of the 482 M. genitalium
> protein-coding genes as essential, plus five sets of
> disrupted genes that encode proteins with
> potentially redundant essential functions, such as

> phosphate transport. Genes encoding proteins of


> unknown function constitute 28% of the essential

> protein-coding genes set. Disruption of some genes
> accelerated M. genitalium growth.
>
> How does atheism account for the origination of the "about 100 genes of
> unknown function" referred to below?
>

> Hutchison III, Clyde A., et al. 1999. "Global Transposon Mutagenesis
> and a Minimal Mycoplasma Genome" _Science_ 286: 2165-2169. The
> abstract, from
> http://www.sciencemag.org/cgi/content/abstract/286/5447/2165?ijkey=4ffdcc413fc0ef90524c454ef65bc5291ed451e8&keytype2=tf_ipsecsha
> Mycoplasma genitalium with 517 genes has the
> smallest gene complement of any independently
> replicating cell so far identified. Global transposon
> mutagenesis was used to identify nonessential
> genes in an effort to learn whether the naturally
> occurring gene complement is a true minimal
> genome under laboratory growth conditions. The
> positions of 2209 transposon insertions in the
>
> completely sequenced genomes of M. genitalium
> and its close relative M. pneumoniae were
> determined by sequencing across the junction of the
> transposon and the genomic DNA. These junctions
> defined 1354 distinct sites of insertion that were not
> lethal. The analysis suggests that 265 to 350 of the
> 480 protein-coding genes of M. genitalium are
> essential under laboratory growth conditions,
> including about 100 genes of unknown function.
>
> ///////////////////////////////////////////////////////////////////////////////////////////////////
> 1985 Cairns-Smith: "Present-day organisms are manifestly pieces of
> 'high technology', and what is more seem to be necessarily so."
> http://groups.google.com/groups?selm=dford3-1123558517.582123.223890%40o13g2000cwo.googlegroups.com
>
> 1985 A.G. Cairns-Smith; How did recorded-in-DNA/ genetic information
> originate?
> http://groups.google.com/groups?selm=dford3-32gv43F3jsrelU1%40individual.net
>
> How does a seeingwatchmakingist account for the origin of
> the recorded-in-DNA/ genetic information within:
> a human? a bacterium? the first biological lifeform?
> http://groups.google.com/groups?selm=dford3-348nj6F47evohU1%40individual.net

Richard Forrest

unread,
Nov 25, 2006, 8:20:48 AM11/25/06
to

What a stupid statement!

Lack of belief in gods is a perfectly respectable way of defining
atheism. It's one of the ways it's defined here
http://en.wikipedia.org/wiki/Atheism, for example. Whether you think
that this is a good definition or not does not alter the simple fact
that it is a common way of defining atheism, so he most certainly is
*not* alone in that "assumption".

RF

Windy

unread,
Nov 25, 2006, 8:21:48 AM11/25/06
to

It's not brain surgery:

ErikW

unread,
Nov 25, 2006, 8:47:09 AM11/25/06
to

Ernest Major wrote:
> In message <1164453446....@h54g2000cwb.googlegroups.com>, ErikW
> <bryo...@hotmail.com> writes
> >> * Some will result from differential gene loss. A gene may be
> >> insufficiently conserved for its homologs in distant relatives to be
> >> recognised, and lost in all remaining close relatives. (This could
> >> happen, for example, in secondarily non-photosynthetic lineages.)
> >
> >It would expect that most complete bacterial genomes are host
> >associated (i.e.human pathogens) and not free living.

Oooh, terrible sentence there from me. Seems you understood anyway. For
anyone who didn't it should read:

"I would expect that most completed bacterial genomes are from host
associated (i.e. human pathogens) and not free living bacteria."

> Parasites often
> >have small genomes since it can use the host for a bunch of things and
> >the same logic should apply to pathogens. I'd expect lots of sequence
> >"decay" and deletions in non-used genes just from this alone and I
> >think that the (potential) bias towards pathogens could be a
> >substantial source of ORFans in the currently available genomes. A
> >prediction would be that pathogens have more non-functional ORFans than
> >free living bacteria. FWIW.
>
> That doesn't seem to be the explanation for ORFans in bacteria in
> general, on two grounds, though the prediction on the relative numbers
> of non-functional ORFans may be valid. Firstly bacteria lose unused
> genes rapidly in evolutionary time, and secondly many bacterial ORFans
> have been demonstrated to be not only functional but essential (in that
> organism).

That sounds reasonable to me. I should mention that I don't really know
much about bacterial genomes though. But since you apparently have have
read some literature about it, may I ask if you've come across any
estimates of the relative numbers of functional ORFans (or the relative
sizes of ORFans, substantially smaller size could indicate
non-functionality) in free living and host associated bacteria? I'm not
asking you to do the work for me, just if you already saw something
like it. It may also be that the distinction between free living and
host associated bacteria isn't that interesting for the reasons you
mentioned above.

>
> On the other hand, parasites, in addition to their tendency to genome
> reduction, also show a tendency to more rapid sequence evolution. Hence
> a bias towards pathogens could introduce a bias towards organisms with
> highly divergent (unrecognisable) sequences, and an overestimate of the
> typical proportion of ORFans in genomes.

Sounds reasonable too.

ErikW

> --
> alias Ernest Major

Larry Moran

unread,
Nov 25, 2006, 8:26:40 AM11/25/06
to
On 24 Nov 2006 16:54:45 -0800, Glenn <GlennS...@msn.com> wrote:
> Uncle Vic wrote:

>> Atheism is the lack of belief in gods. That's all.
>>
> You are very alone in that assumption.

No, he isn't.

http://sandwalk.blogspot.com/2006/11/agnostics-are-whimps.html

But see ...

http://scienceblogs.com/evolvingthoughts/2006/11/agnostic_still_1.php

Larry Moran

Ernest Major

unread,
Nov 25, 2006, 10:19:43 AM11/25/06
to
In message <1164462429.6...@f16g2000cwb.googlegroups.com>,
ErikW <bryo...@hotmail.com> writes

>But since you apparently have have read some literature about it, may I
>ask if you've come across any estimates of the relative numbers of
>functional ORFans (or the relative sizes of ORFans, substantially
>smaller size could indicate non-functionality) in free living and host
>associated bacteria? I'm not asking you to do the work for me, just if
>you already saw something like it. It may also be that the distinction
>between free living and host associated bacteria isn't that interesting
>for the reasons you mentioned above.

I haven't seen this addressed directly. It's not obvious that it can be
addressed with the current dataset. (You'd have to control from the
effects of non-random taxonomuc sampling.)
--
alias Ernest Major

Richard Clayton

unread,
Nov 25, 2006, 10:31:23 AM11/25/06
to
Glenn wrote:
> Free Lunch wrote:
>> On 24 Nov 2006 16:54:45 -0800, in talk.origins
>> "Glenn" <GlennS...@msn.com> wrote in
>> <1164416085.3...@j44g2000cwa.googlegroups.com>:
>>> Uncle Vic wrote:
>>>> Once upon a time in alt.atheism, dear sweet david ford (dford3
>>>> @gl.umbc.edu) made the light shine upon us with this:
>>>>
>>>>> can atheism account for origination of 382 essential genes?
>>>> Atheism is the lack of belief in gods. That's all.
>>>>
>>> You are very alone in that assumption.
>> Hardly.
>
> No, not hardly. Vey alone.
>> Why do you claim it means something else? It certainly has nothing to do
>> with science.
>
> Neither did the question use the word science, nor did I say it "meant
> something else". A lack of belief is not all atheism is. Atheism is
> also a belief that there is evidence against the existence of God.

I think you're using the word with a non-standard meaning. I'm an
atheist, but I can't think of any evidence AGAINST the existence of *a*
god. Or, for that matter, *the* God, though when different people talk
about God they often attribute very different characteristics to Her.

How could you provide evidence against the existence of an entity with
unknown but vast powers that do not operate within the known bounds of
scientific theory, and with unknown motivations and goals?

I do agree that some self-described atheists seem to have a serious
grudge against the religious, possibly because the most vocal segment of
the religious demographic often comes across as a pack of hateful,
irrational sociopaths. I wish the religious moderates (whom I believe to
be in the majority) would speak up and stop giving the Pat Robertsons
and Jerry Falwells free reign. And for that matter, I wish Richard
Dawkins would confine himself to empirically testable science.
--
[The address listed is a spam trap. To reply, take off every zig.]
Richard Clayton
"During wars laws are silent." -- Cicero

Richard Harter

unread,
Nov 25, 2006, 11:00:25 AM11/25/06
to
On 25 Nov 2006 05:20:48 -0800, "Richard Forrest"
<ric...@plesiosaur.com> wrote:


You are misreading the statement. By not believing in gods you are
alone in that you do not have the company of gods, at least of the sort
that will not intrude upon your disbelief.


Bob Casanova

unread,
Nov 25, 2006, 4:41:38 PM11/25/06
to
On 24 Nov 2006 11:35:26 -0800, the following appeared in
talk.origins, posted by "david ford" <dfo...@gl.umbc.edu>:

<snip>

>Dr Forrest, how does atheism account for the origination of those 382
>essential genes?

The same way that biologists account for the words used in a
Pater Noster.

Idiot.

<snip>
--

Bob C.

"Evidence confirming an observation is
evidence that the observation is wrong."
- McNameless

Glenn

unread,
Nov 25, 2006, 4:49:02 PM11/25/06
to
Larry, you argue that atheism is not all simply a lack of belief.

Christopher Heiny

unread,
Nov 25, 2006, 11:42:36 PM11/25/06
to
Glenn wrote:

> That's not true, for anyone. 6 million or more years to evolve two
> primates that appear almost identical, and 50 million years to go from
> virtually a single cell to a fish, doesn't match up any where close.
> That's why there are these theories of catastrophic events, cosmic ray
> storms, oxygen increase, etc. increasing this "gradualness" most
> significantly.

The earliest trace fossils indicating multicellular life are about 1.1
billion years old (Science, September [I don't recall the day, sorry]
1998), though my memory may be faulty here.

Ediacaran multicellular fossils date from the late Precambrian, 565 to 543
million years ago.

The earliest fish date from the Devonian, 410 to 360 million years ago (once
again, my memory may be faulty).

So we get 155 million years as the minimum from the first indubitably
multicellular life to fish (though there is no reason to believe that the
Ediacaran fauna are ancestral to fish), and about 700 million years from
the first potential traces of multicellular life.

--
Christopher Heiny
Professor of Bizarre Theories
University of Ediacara

.

Glenn

unread,
Nov 25, 2006, 11:51:31 PM11/25/06
to
Amazing. Single-handedly discounted the whole concept of the Explosion.

Bob Casanova

unread,
Nov 26, 2006, 3:56:56 PM11/26/06