Thursday, October 22, 2009
He's been peddling this claim - and refusing to budge despite having been corrected by at least 4 professional biologists that I am aware of - for about 8 years.
Briefly, humans have 46 chromosomes, while the other great apes have 48. There is evidence that human chromosome 2 arose via a fusion of two other chromosomes, and that is why we have 46. Ilion claims that even if thi sfusion occurred, 2 problems arise - 1. depressed fertility and 2. the fixation in the population (not enough time, or something).
The short answer is, the human chromosome 2 fusion is not really an issue.
And we can say this by looking at living mammals who do perfectly well with altered karyotyopes fixed in their population (even some that maintain polymorphic karyotyes, which Ilion insists is a bad, bad thing and essentially impossible).
Let's look at one example.
The domestic horse has 2n=66. Przewalski's horse has 2n=64. The difference is a fission of the domestic horse's chromosome 5 (or a fusion of 2 of P. horse's chromosomes forming the domestic horse's chromosome 5, if you like).
Here is the clincher - they can interbreed and produce fertile offspring.
But they are not odd numbers you say?
OK - let's stick with horses.
The Caspian pony maintains a polymorphic karyotype.
Some are 2n=64, some are 2n=65, and they get along smashingly.
Ilion the computer tech's arguments are just mantras and nonsense.
Friday, October 16, 2009
A blast from the past:
I have written briefly about Troy D. Hailey before - a computer consultant who fancies himself an expert on, well, everything, but especially evolution (claims, as they all do, to have "disproved" it).
Well, it seems that even his fellow computer programmer-type folks are not very keen on the condescending, arrogant egomaniac.
Seems old Troy didn't dig it that all did not bow down to his superior intellect, and began a flame war of sorts, with the admins and participants at the board trying to decide how best to deal with him:
Chris Maunder wrote:I'm ready to just close it [the 'soapbox' forum] up
That's what Ilion wants. It seems that most - if not all - of the SoapBoxers are united in their opinion of the Ilion person. What you probably should do is find out who this guy's ISP is and report him for abuse,and then block the ISP's IP subnet from being allowed to post on CP.
In response to thje above:
John Simmons / outlaw programmer wrote:That's what Ilion wantsAnd to see that arrogant 'charm' from old Troy the self-identified 'nobody' (he is so humble...):
Actually it isn't. What he wants is to be able to post his opinions and have them stay in view and not be voted as abusive. Whether or not his posts are abusive, spam, or even vaguely appropriate is another thing.
My understanding was that people were ignoring him, so he repeatedly startedposting the same thing and THEN they were marked as spam/abuse.
Chris Maunder wrote:Of course you do, as long as you do not abuse the forums or the site.Wait - there is more (emphasis mine):
Mr Maunder, you've giving mixed signals here.
On the one hand, I should "probably just move on" if I want to try to discuss thing rationally/logically, because it's "abusive" (as per community consensus) to identify the illogical arguments/assertions others make.
On the other hand, if I'm not "abusive" (i.e. if I insult other persons right and left, as per community practice), then there is no difficulty.
I gotta tell ya' that's dizzy-making. To me, at any rate.
Look, most of the really active regulars here go out of their way to express contempt for Christianity and for Christians. And that's ok, I'm not complaining; Christianity can take it. And I can take it, so long as I'm allowed to demolish the so-called arguments.However, because I am trying to get at the illogic and/or absurdity of so many of the claims and/or arguments put forward on the anti-Christianity side of the ledger, I am apparently "abusive," as per community consensus. It isn't true in fact, and I do not appreciate it.Because after all, a computer cunsultant expert on everything cannot do anything BUT "demolish" all arguments of those that dare oppose his ideologies...
Now, if 'atheism' and/or 'atheistic' assertions have a privileged or protected status here at CP, I can live with that. As I told you, I came to CP for the programming, not for the Soapbox. However, it would have been nice to know about that special status beforehand.
But, it goes on.. and on...
He's [Ilion] taking you for a ride Chris. If you trace back through the threads, you'llfind he was given ample opportunity to expound his arguments and he declined totake them. People, myself included, attempted to dispute points with him (despite his sillyness), but it was to no avail. When everyone began to ignore him (and rightly so) that's when he started bombing the forums. Despite his claims and protestations, he was treated no differently than anyone else. The difference was in him refusing to cease his obnoxious behaviour and his blatant disrespect for ALL PATRONS of this forum. On numerous occasions did several others and I ask him to stop yet he continued. I suggest you continue to monitor this forum for the next few days as I don't believe he is being genuine.
[I grew tired of trying to fix links at this point, but you get the picture...]
I am not sure what is worse, the constant posts by Ilion, or our response to it.Some of his messages have been deleted under 10 minutes. They are literallybeing removed before I can read them, although they seem to be the same 1 or 2posts over and over. I don't get what his point is, and I don't get why we don'tignore him. I don't remember Ilion posting before a week or so ago. He has fourarticles (I have not read any) and all of a sudden of deluge of incomprehensibleposts. I think we have all agreed that something is wrong mentally (some kind ofpsychotic break?), but do we need to poke the badger with a spoon?
A thread for Ilion to demonstrate....his much touted great intellect.Apparently you believe yourself to be beyond the intellectual capabilities of everyone on this message board. Well, I'm giving you the opportunity to prove it. Answer our questions, the ones that (so far) you refuse to answer. There are many of them, but you seem to believe it acceptable to make flippant statements without having to provide any form of cogent argument. Well, I'm putting you on the spot. Either prove you have something to contribute or finalize that once and for all that you're just here trolling these boards to irritate people and you are not to be taken seriously. Show us you're not a cheap pathetic hack...
It is interesting to note that Ilion did not reply once in that thread...
He [Ilion] was annoying me because he was intentionally twisting my words.Having an argument with somebody is one thing. When somebody twists your wordsto deliberately misrepresent what you said is another. I have a problem withliars and hypocrites. I call them out. Ilion knows he's lying and deceitfulbecause he doesn't respond to my posts. He thinks he's a Christian - but it'scompletely obvious he's a hypocrite and a liar. He's less of a Christian than Iam and I'm an athiest.
Oh - you noticed all that, too?
Poor Troy Hailey - he can't even seem to get his fellow computer geeks to be on his side and bow down to his ubermensch status!
Because people like Ilion will just never let things rest. They HAVE to have it "known" that they "won", that they are "right". Even when they are not.
It is interesting to note that on that site, even the conservatives (well, one of them at least) thinks Ilion is a nitwit:
Ilíon wrote:Man, that's jest terrible! Political appointees being treated as political appointees.
Redstateler:You know, I read that and thought something odd. The "e" key is nowhere near the "u" key on a keyboard, so how could you mistype "just" (as a typo) unless you're so hopped up on acid that you have no control of your fingers.
He is, of course, welcomed with open arms on the ARN'>http://www.arn.org/ubbthreads/postlist.php?Cat=0&Board=13">ARN 'Intelligent Design' forum - that is the sort of person that makes up the anti-evolution crowd - arrogant, overconfident, bombastic, and above all, underinformed. So, how can these folks deal with the arrogant blowhard?
I have an idea:
Stop talking out of your ass. Everyone on this message board is sick to death ofyour idiocy. Do everyone a favour for once and shut up. It's painfully evident that you don't know a thing about science, you just like to run your mouth and stick quotes around everything. Take your medication. It'll help to make you more lucid. You can't even address the questions I put to you, because when confronted head on you balk and hide. You're pathetic, ignorant and an idiot. That's quite the amazing combination, you should be proud. Not just anyone can achieve such infamy. Of course, you can always respond to the thread I directedat you and prove me wrong, but I know you won't because you can't. You're a sadlittle man with an inferiority complex. I pity you. If only you had the sense torealize just how idiotic you are, it would be a blessing for you AND thismessage board.
Boy - these folks figured Ilion out, alright!
And Ilion is God's one true messenger... Wow....
Some things never change....
Friday, August 14, 2009
Over on HuffPo, Barrett Brown wrote this article:
Intelligent Design, Online Edition
Sundry Dembski worshippers flocked to HuffPo from UncommonDescent to defend their Ideology. It appears that many of them, including one 'Uprightbiped' - were on autopilot, and responded to the article by complaining that Brown did not discuss the (pseudo)science of ID.
But you see, the article was about ID on the internet, specifically, how Dembski runs his blog and how he is a hypocrite, which any sensible, rational, intelligent person could see form actually, you know, reading the article.
But not Uprightbiped. Nosirree. You see, he thinks that because the title of the article had the phrase "Intelligent Design" in it, it is supposed to be only about the 'SCIENCE' of ID and nothing else.
And so, Uptightbiped decided to reply by first whining about how Barrett did not specifically discuss ID and how all he did was 'condemn' Dembski - which, amazingly, the ARTICLE WAS SUPPOSED TO BE ABOUT!!!
See for yourself:
Virtually every comment on this post has nothing whatsoever to do with ID -
neither does Barrets trivial condemnations of Dembki. One of the commenters here
visited Demski's UD site, stomped his feet and said "Where is your inference
coming from? Upon what scientific facts is ID based?"
For those who would rather KNOW than be just another link in the chain, you might
consider reading David Abel's peer-reviewed paper in the Journal of Theoretical
Biological and Medical Modeling. He spells out the case in no uncertain terms.
Its available here: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1208958There is also another from the International Journal of Molecular Science: http://mdpi.com/1422-0067/10/1/247/pdfOne thing is for
certain, no one here will address the evidence presented in either of these
peer-reviewed journals on its face. Building strawmen, as Barret has done, is
always more fun.
I guess I should also mention that Uptight (yeah, I know, namecalling - well, he took to calling me 'Scotty' at HuffPo, I guess that was supposed to be an insult, so back at ya, Uptight) seems as enamored with creationist David Abell as he is with Dembski.
Of course, Uptight's original post did not even acknowledge what Brown's article was really about. So, I replied:
Isn't is amazing?
A piece NOT actually intended to be about the vacuous
gobbledegook that is "ID" has nothing whatsoever about 'ID" in it!It is a
conspiracy, I tells ya!
Pro-ID zealots are a constant source of entertainment, to
And it went on from there, with Uptight engaging in the usual hero protection and false accusations that I have grown accustomed to seeing from these people when things don't go there way.
In the end, his posts were little more than focused and constrained Gish gallops and argument via false authority. See for yourself, in toto, starting after my reply above:
Scott, Here is what is amazing: A peer-reviewed article appearing in the Journal
of Theoretical Medical and Biological Modeling, and a companion piece in the
International Journal of Molecular Sciences implicitly states:"The fundamental
contention inherent in our three subsets of sequence complexity proposed in this
paper is this: without volitional agency assigning meaning to each
configurable-switch-position symbol, algorithmic function and language
will not occur. The same would be true in assigning meaning to each
combinatorial syntax segment (programming module or word). Source and
destination on either end of the channel must agree to these assigned meanings
in a shared operational context. Chance and necessity cannot establish such a
cybernetic coding/decoding scheme ."
"To focus the scientific community’s attention on its own tendencies toward overzealous metaphysical imagination bordering on “wish-fulfillment,” we propose the following readily falsifiable null hypothesis, and invite rigorous experimental attempts to falsify it:“Physicodynamics cannot spontaneously traverse The Cybernetic Cut :
physicodynamics alone cannot organize itself into formally functional systems
requiring algorithmic optimization, computational halting, and circuit
"A single exception of non trivial, unaided spontaneous optimization of formal function by truly natural process would falsify this null hypothesis".
...and so you suggest this has nothing to do with the hypothesis that volitional agency is required to achieve function in the sequencing of nucleotides.Nice. What exactly did you think the author was talking about when he said the phrase “volitional agency”?http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1208958
One will note that he replies as if I had responded to him specifically about his links, which I did not. Specifically the last paragraph - Uptight seems to have me confused with others (which he basically admits later, but will not directly acknowledge). I reply:
Interestingly, your reply does the same thing to me that your earlier reply
did to Brown's article. It ignored it. That or you got me confused with someone
Perhaps if I use simpler language - Brown's article was not about the lack
of scientific merit of ID, or even of ID in general, rather, it was about Bill
Dembski and his antics. Why did you expect his article to address ID when it was
not about ID?
And why would you have expected my reply to you to be about the
bafflegab-riddled articles that Trevors and Abel somehow got published when all
it was intended to do was point out that your earlier response was essentially a
But since you are so enamored with Trevors and Abel, perhaps you can
explain how it is that an objective reader should take their claims seriously
when ALL of their 'conclusions' are premised on a totally unsupported assumption
that the genetric code was 'written'?
One will also note that despite his obvious adoration of Trevors and Abel, Uptight does nto once even try to answer my challenge in the last part. I continued:
Their 2004 paper contains this as a premise:
"How did inanimate nature write:
1. the conceptual instructions needed to organize metabolism?
2. a language operating system needed to symbolically represent, record and
replicate those instructions?
3. a bijective coding scheme (a one-to-one correspondence of symbol
meaning) with planned redundancy so as to reduce noise pollution between triplet
codon "block code" symbols (bytes) and amino acid symbols?... "
Fails from the get go.They start by assuming their conclusion - that
metabolism/genetic code was pre-planned and written, and that "inanimate nature"
cannot do this.
Theirs is an argument via analogy combined with an argument via defintion
combined with an argument via personal incredulity, gussied up with some
superfluous jargon and 'information theory' gibberish.
What about this peer reviewed scientific paper:Natural selection as the
process of accumulating genetic information in adaptive evolutionM.
KimuraGenetical Research (1961), 2:127-140 Cambridge University Press
Kimura demonstrated mathematically that adaptive evolution adds information
to genomes. Wonder why TnA never mention that...
I should also note the last sentence of the liked paper:"We invite potential collaborators to join us in our active pursuit of falsificationof these null hypotheses."In other words, they've just tossed out some hypotheses. Which is fine. What is not fine is that their acolytes then proceed to present these hypotheses as some sort of unfalsifiable truths.
Scott, (Part 1)
You say: “Interestingly, your reply does the same thing to me that your
earlier reply did to Brown's article. It ignored it.”
My comment was targeted directly at the posts being
made in this forum. This might have been obvious by the first words of my
post, which were “Virtually every comment on this post…” And by the way, I noticed in your first post you suggested the paper I cited had
nothing to do with the inference to volitional agency – and in your
second post you’ve seem to have abandoned the claim.
You say: “Perhaps if I use simpler language - Brown's article was not about
the lack of scientific merit of ID…Why did you expect his article to address ID
when it was not about ID?”
An article with the words “Intelligent Design” in the heading isn’t about
An article that suggests that ID proponents “can't get away with trying to
portray ID as a scientific theory” does not attack the “scientific merit” of ID?
So, having had to abandon your original comment as factually untenable, you’ve
been left to make observations that are demonstrably incoherent.
Tell me why anyone should take these observations of yours seriously.
Interesting... I've highlighted (in red) some interesting, if not unwitting, 'admissions'..
For how did I 'abandon' a claim I never made? Note also that Uptight has attempted to diminish anything I might write - I mean, why would anyone take me seriously when I abandon a claim I never made, right? One will see that, in typical IDcreationist fashion, Uptight later essentially accuses me of doing the same thing to his poor heroes...
If your comment was directed at other posts, why reply directly toIn the threaded world of blog replies at HuffPo, things get a little hairy, as Uptight also reponded with this:
You write:"And by the way, I noticed in your first post you suggested the
paper I cited had nothing to do with the inference to volitional agency – and in
your second post you’ve seem to have abandoned the claim."
In my first post, I mentioned or implied nothing of the sort. In fact, I
did not even MENTION anything you had written - you seem to be coflating again.
The SOLE purpose of my first post was to point out that you, as have
several other anti-'Darwinists', lamented that Brown did not discuss ID when the
fact of the matter is that was not the intent of his article!
You go on, as ID advocates are wont to do:
"An article with the words “Intelligent Design” in the heading isn’t about
“Intelligent Design”. ... So, having had to abandon your original comment as
" you’ve been left to make observations that are demonstrably
"Tell me why anyone should take these observations of yours
So, if the article has the phrase "Intelligent Design" in the title, it
must by some magical set of unwritten rules, be solely about ID in toto?
Please demonstrate how my comments are incoherent - I realise that to the
anti-'Darwinist', mere assertions count as irrefutable evidence, but to rational
folk, that won't cut it.
Then you say:
“And why would you have expected my reply to you to be about the bafflegab-riddled articles that Trevors and Abel somehow got published when all it was intended to do was point out that your earlier response was essentially a non sequitur?”
Your original post was nothing but a petty ad hominem
attack on ID which made absolutely no mention of a “non-sequitur” in my
comments, nor did it provide any rationale that supported the idea that one
existed. You are digging a hole.
In truth, you portrayed my comment as “gobbledegook” trying to extort
a peer-reviewed paper as having anything to do with ID, and then after being
corrected you switched to portraying the Abel paper itself as “bafflegab”.
You even go so far as to imply that the peer-review process at the
International Journal of Molecular Science, and that at the Journal of
Theoretical Medical and Biological Modeling, should perhaps be called into
question. What is most clear is that amidst all of your repeated attempts to
slander the reputation of anyone that disagrees with you, you say nothing
whatsoever about the actual evidence.
Why is that?
“But since you are so enamored with Trevors and Abel, perhaps you can
explain how it is that an objective reader should take their claims seriously
when ALL of their 'conclusions' are premised on a totally unsupported assumption
that the genetric (sic) code was 'written'?”
Surely you are kidding? You are actually objecting to the completely common
phrase that the genetic code was “written”? Well, if that is your objection,
then you need to get your objection pen out.
You are going to be busy…“…genes were written in a code…” -Cornell
“…DNA sequence, as a book written in a special code…” -Michigan State
“…a text written in a language common to all life…” -Nat Geo
“…a code written in multiples of three bases…” -Nature“
…a sequence of words written in the alphabet A,C,G,T…” -Carolina
Truly you can’t be serious. Trevors and Abel used the
term “written” in the exact same way as the authors of the text above –
and it is an abject lie to suggest otherwise. So not only must you try to
slander the reputations of those scientists that disagree with you, you also
must misrepresent their work in order to do so.
Poor Uptight's heroes, so in need of his protection - so much so, that Uptight, as IDcreationists so often do, felt the need to drum up some well poisoning and false accusations against me. That is what these people do. One will note that other than admit that he takes metaphorical langauge literally, he never does actually show how Abel's claims have merit.
Of course, when one bothers to learn a bit more about Trevors and Abel, one finds that, in fact, they are not at all using the term "written" in the exact same way those other sources are. I guarantee it, and it is obvious for the loaded language that TnA use. But Uptight and his creatinist cronies turn off their BS meters when reading wrok from 'friendlies'...
But he goes on:
Finally, you say:
“They start by assuming their conclusion - that metabolism/genetic code was
pre-planned and written, and that "inanimate nature" cannot do this. Theirs is
an argument via analogy combined with an argument via defintion combined with an
argument via personal incredulity, gussied up with some superfluous jargon and
'information theory' gibberish.
Your finale is one long mischaracterization followed by a few ad hominem
arrows thrown in for flavor. Yet, never do you actually
address anything of the observable evidence at the molecular level
(almost none of which is even in doubt by scientist of any stripe). Nice defense
there, Scotty- - - - - - -
By the way, Kimura’s demonstration assumes
replicating/metabolizing cells. Abel didn’t mention it because it has
nothing to do with origins research (since it already assumes
Never mind that TnA never actually mention any evidence - their papers are are purely hypothetical. So, I respond:
Ah, the old creationist stand bys - "ad hominem!" "misrepresentation!"
"You're being mean to my hero!"Calm down, fella.Surley, you know what
metaphorical languiage is, yes? I am fairly certain that the authors of your
sound bites do not think that the genetic and such were 'written' the way
creationist Abel and his pals do.
So, you read Kimura's paper did you? I did not mention any of the 'evidence' at
the molecular level at T and A do not actually present any.The fact is, the only
people who take their work seriously are themselves and a handful of
IDcreationist types, as evident from the dearth of citation.
Uptight didn't like that much, but he, perhaps, realized that he was in over his head and decided to bow out:
I didn't reply to you - Scott, ...you REPLIED to MY comment.
See how that works?In fact, you have now posted on my comment seven seperate times. Yet, you haven't addressed the actual content of my post even once, and indeed, in the your latest post you continue to attack everything but the evidence. I am willing to allow any readers to make of that what they will.
By all menas you may have the last word.
But I'll bet he's a regular HERO at Uncommondescent!
Note that in the world of the IDcreationist, quotes and disbelief that you don't agree with them count as a demonstration that their sources are correct.
Unlike the hero-worshipping Uptight, I plan on actually responding to what he has written. It might take me a few days (pretty busy this timie of year), but I'll get to it.
Thursday, August 13, 2009
HuffPo is hardly the place to engage in any real discussion, due in part to the limit of 250 words. But if you think Trevors and Abel's work is so great, let's see your stuff.
Be forewarned, however - false charges of 'ad hominem' and the like will not fly. Assertions do not work here. Argumentum ad verecundiam will not work here.
Thursday, January 29, 2009
A few months ago, Jeff Shallit wrote about an article in The Scientist, and it got creationist Kirk Durston's attention.
I won't go through ANY of the details - Durston, like many creationists, prefers overly verbose rhetoric to concise language, but feel free to slog through all his patronizing gibberish if you'd like. Others dealt with the technical details of Durston's claims, but I found this short statement very informative:
The question is, is the functional information encoded in the gene that codes
for RecA an example of ID? (I choose RecA because it is an average length
protein, it is a universal protein found in all life forms, and I've done some
work on it.) To answer that question, we need a scientific method to identify
examples of ID that does not yield false positives, yet does not rule out
obvious examples of ID (such as Venter's 'watermarks', or laptop computers) and
is general (i.e., can be applied to forensics, SETI, archeology, and biology).
When I read this (re-read it, actually - I had read the entire exchange some months ago) this really struck me as profound.
And maybe I am just slow and others ahve already recognized this, but it seems ot me their entire line of reasoning regarding "informaiton" and how evolution cannot account for it rests on one little subtle assumption. But it is a big one - a great big foundational assumption which makes their entire 'no new infromation' enterprise little more than a tautology.
Can you see it?
It isn't about ID detection methods or the arcane mathematical details that accompany his boasts. It is this:
...is the functional information encoded in the gene that codesfor RecA an
example of ID?
The functional information ENCODED IN the gene.
Why would they think it is intelligently derived? Because that start out with the a priori position that the 'information' that the gene contains/possesses was PUT IN IT. It is ENCODED:
–verb (used with object), -cod⋅ed, -cod⋅ing.
to convert (a message, information, etc.) into code.
And how is this 'conversion' done if NOT by an intelligent agent, right?
They start out with the assumption that a gene did not arise via natural means and by virtue of the arrangement of it's nucleotides and ends up producing a useful protein, no they start out assuming that a specific protein was needed/desired and that the gene was then 'somehow' acquired in order to make this needed/desired protein.
In other words, they start out assuming what they want to be true.
To be fair, I suppose one could say the same of non-IDcreationists. They start out with the assumption that genes are natural entities, polynucleotides shaped by natural forces into a gene that when transcribed and translated makes something useful.
The difference is, the IDcreationist has mere faulty analogies to support their position.
'Materialists' have observation and experimentation.
Sure, Mike - and every other Republican sycophant.. Admire away.
What is not to admire - and take marching orders from - a draft dodging coward like Limbaugh?
A family-values advocate with 3 divorces under his belt.
A good Christian man wio smuggles Viagra to the Dominican Republic. Why would he do that? He wasn't married at the time, so he didn't need them for intramarital relations. Must have been for the underage male prostitutes that the Dominacan Republic is known for.
Blow him some kisses, Mike! Maybe he'll take you with him next time.
And I won't even mention his addiciton to Hillbilly Heroin...
I think it says quite a bit about the people who would 'admire' and 'respect' such a pathetic hypritical pile of filth like Limbaugh.
Tuesday, January 20, 2009
Now, I've read some of Coppedge's stuff before, but I'd not visited his site for some time, so I decided to pay a visit and I was reminded of why I hadn't been there in a while - to describe the site as inflammatory is putting it mildly. I searched his site for some issues of interest to me, and no surprise, I was soon rewarded with a number of highly misinforming/disinforming smug dismissals of legitimate science and that characteristic cherry-picking of quotes to employ as 'look how little evolutinists know!' fodder.
And let us not forget his condescending name calling and the like.Take a look at this masterpiece of flim flammery, sleight of hand, and inflammatory disinformation, my comments interspersed:
The Hopeless Task of Building Evolutionary Trees
A paper posted in the online early addition July 25 of the Proceedings of
the National Academy of Sciences starts out with an optimistic subtitle: “An
efficient solution for the problem of large phylogeny estimation,” but then
opens with a tone of despair:
Optimality criterion-based phylogeny inference is a
notoriously difficult endeavor because the number of solutions increases
explosively with the number of taxa. Indeed, the total number of possible
unrooted, bifurcating tree topologies among T-terminal taxa ... [corresponds] to
nearly 32 billion different trees for 14 taxa and 3 X 1084 trees (i.e., more
than the number of atoms in the known universe) for 55 taxa. ... As most
mathematicians expect that no such algorithm [i.e., polynomial time solution]
exists, one is forced to admit that no future civilization will ever build a
computer capable of solving the problem while guaranteeing that the optimal
solution has been found.
Instead of number-crunching the impossible, the authors propose a heuristic
approach. Heuristic approaches sacrifice the goal of getting an optimal tree in
hopes of getting one faster that has maximum likelihood (ML).
Um, no... I would think that a taxpayer-funded NASA "scientist" like David Coppedge would at least try to understand the material he is bashing, but I guess that is too much to ask of a creationist. Even a NASA employee. The whole point of a heuristic search is still to find the optimal tree, but to do so without having to examine every single possible arrangement of taxa.
Can a 'computer geek' like Coppedge really not know this?
As this applies to phylogeny searches, look at it this way (A spectacularly simplified example) - say you have DNA sequences from 4 taxa and you want to do a phylogenetic analysis. Their sequences are:
We can note that sequences 1 and 2 differ by only one substitution; 1 and 3 by two; 1 and 4 by 8; etc., and we know that taxon 4 is not closely related to the other three. If we choose to root our tree (that is, if we recognize that one of the taxa in our analysis will be the most distantly related to all the others), there are 15 possible arrangements that could be produced (we can quickly see which taxon this is going to be, but we would want to test each one to be sure). Now, we could simply draw out all 15 possible arrangements, count up the number of nucleotide changes needed to 'describe' each tree, then pick the tree with the fewest changes as our optimal tree. But that would take, if we use 5 minutes drawing and calculating each arrangement for our example, 75 minutes. Now, if we employ a heuristic search algorithem, we do not draw and calculate every possible tree, because we can immediately discard 'bad' trees/arrangements without having to draw and calculate them.
For example, a quick comparison of each pair of sequences tells us what I wrote above ("We can note that sequences 1 and 2 differ by only one substitution...") and we can use this information, which can be generated in much less than 5 minutes, to see which groupings are the most likely. In our little example here, we can see that taxa 1 and 2 are the closest, with taxon 3 joining the group of 1 and 2, with taxon 4 as out outgroup. So we know that taxon 4 will be the outgroup, therefore, we only have to draw and calculate how taxa 1, 2, and 3 should group. And as we established that taxa 1 and 2 are the closest, there is only one tree that will do. This can be calculated in maybe 10 minutes, if we do it by hand, and use the "heuristic" I just described, which is essentially what computer analysis programs do (albeit, obviously, with much more rigor).
Coppedge is just trying to use the classic creationist "argument via big numbers" and relying on the fact that most of his acolytic readers will not know any different.
Further, maximum likelihood is a search criterion, not an intrinsic value.
Coppedge is clueless. Perhaps for real.
Lemmon and Milinkovitch wrote a computer program that converges quicker on an ML model with larger number of taxa. They call theirs the “metapopulation genetic
algorithm.” It is a quasi-Darwinian model that tries to optimize trees based on
mutations and selection, and it can incorporate rate heterogeneity estimates
into the model. The authors try their program on real and imaginary populations
and compare their results with other heuristic methods.
The article in question came out in 2002. Coppedge writes as if such an algorithem is a new thing. To put this in perspective, I entered graduate school in 1999, and I started out using a computer analysis package that utilized maximum likelihood methods (as well as about 4 others) that was written nearly 10 years earlier. Below is Coppedge's snarky disinformative commentary:
Were you ever told in biology class that generating a phylogenetic tree from the
raw data was mathematically impossible, and that no future civilization would
ever overcome this barrier? Probably not, yet textbooks are replete with neat,
authoritative-looking phylogenetic trees. So how do they determine them? By
heuristic methods, which by translation, means guesswork, inference,
trial-and-error, hunches and hope. Their model incorporates a number of
optimization parameters, such as rate heterogeneity, which means that not all
genes mutate at the same rate, and branch length, the presumed evolutionary
distance between taxa.
Wow... Where to begin? No, Coppedge, heuristic methods do NOT at all mean "guesswork" etc. And for a NASA employee to denigrate trial and error??!?!?? Is he for real? One of my interests is spaceflight, and I have seen many programs about the space program, and NASA's history is little BUT trial and error! And the shock of a program incorporating rate heterogeneity! Imagine, incorporating what the evidence indicates! I have little doubt that one can find on Coppedge's site some snarky little essays decrying any notion that all genes mutate at the same rate. And as far as branch length goes - the programs FIND the branch length as part of the analysis! How can it incorporate something that is one of the outputs of the algorithem!
This guy is CLUELESS!
The tweak space is enormous, and they already have a mental picture of what they
want, so this whole approach is based on circular reasoning. If the program
outputs a tree that agrees with the evolutionary assumptions, is scores high;
otherwise, it is rejected.
Amazing. Coppedge - who should at least have a basic understanding of the terminology (since things like "heuristic searches" are common computer science terms) , is simply spouting nonsense. I challenge anyone here to read the actual paper and point out where the authors state that they already 'have a mental picture of what they want' and somehow force the program to spit out this desired result. The entire purpose of the paper in question was to outline the authors' procedure for producing phylogenetic trees using large datasets with many, many taxa more quickly than can be done with existing methods. Coppedge acts as if they are merely trying to find a way to make a program that produces what they want it to (he must be confusing real science with baraminology).
Of course, what they set out to do - to make a computer analysis program that can analyze large numbers of taxa in large datasets more quickly and just as accurately as existing but slower models all but requires them to 'know' what they want to get - that is how you test your model! Does Coppedgfe REALLY not understand this?
Does this provide any confidence that evolution is being confirmed empirically?
Is this how scientists in our universities should be spending their time,
playing Darwinian computer games?Instead of explaining how mutation and natural
selection could produce a Monarch butterfly or a finch or a peppered moth in the
first place, scientific papers on evolution seem obsessed with trying to uncover
phylogenetic relationships that are impossible to calculate objectively or
verify independently without begging the question whether common ancestry is
Is this how a taxpayer-funded NASA scientist should be spending his time -writing disinformation filled drivel to prop up his religious beliefs?
And the coup de grace - Coppedge at his sleight of hand best. We see this silly sentiment in many creationist rants - this whole 'those evos are ASSUMING evolution is true when they do their experimets!' as if that is a bad thing to do.
Do creationists assume creation is true when they do their experiments (I mean, if they did any)?
Do physicists assume that gravity is a constant throughout the universe when they plot spacecraft flight paths?
Of course they do - why, I'd even bet that NASA computer technicians like Copppedge assume certain things about the software writing programs they utilize and the models they make.
I would like to point out that this distortion-laden diatribe was one of the shortest I could find on Coppedge's site on this subject. I can only assume that longer rants have even more distortions and embellishments. But David Coppedge need not be concerned -his like-minded readers will believe everything he writes - he is a YEC AND he works at NASA, after all - and will think his smug insults are all well deserved by those evilutionists.
Wednesday, January 14, 2009
I recently got a comment on my blog and I would love to share it with you. I will leave the name of this individual anonymous but see if you can see what is missing in his comment."I appreciate the spammed post on my blog. I deleted one and posted the other. No Darwin did not have an electron microscope, nor did he know about DNA. Had he, I predict that the would have really enjoyed the vast amount of evidence supporting his basic premise that one can find there". (Which this person commenting does not mention here!!!). " Are cells simple? Not really(not really, look at your science not at all!!!). But simply arguing that they are so complex that could not have arisen by 'chance' and thus evolution is false thus biblical creationism is true is just wrong on so many levels." (yet he does not mention or give facts stating how it is wrong!!) "And I wouldn't be so quick to trust the claims by the folks at ICR in the first place (which he offers zero evidence why other than they disagree with his ideology).- they require al of those associated with them to take oaths that they will never cast doubt on creationism (simply not true), and have a pretty good tract record of having their, shall we say, less than honest antics exposed (Which again he fails to mention one single occurrence.)Did you see what was missing throughout this man's whole entire argument?? Facts? Again where are the facts, he has been reduced to name calling and empty allegations. Offer me one proof of anything you say. Read my blog post simply not simple in which I quote Charles Darwin!! Yet he offers zero evidence on which his position stands. Then the evolutionist like this man have the audacity to claim that we are the ones who believe in blind faith, who have no evidence. DNA has the amount of info to fill 500 books with a 1000 pages each, an incredible amount of information on a molecular level. Where does this information come from?? How would Darwin be overjoyed if he had an electron microscope?? WHat is it within a cell supports organic evolution?? Darwin himself said the opposite, he said "if it can be demonstrated that any complex organ exited which could not have possibly been formed by numerous, successive, slight modifications, my theory would absolutely break down". (Origin of species) 1872, p.154So this man who commented said Darwin would be overjoyed, when he himself wrote the quote above which is exactly what we see in a cell. Darwin wouldn't be overjoyed, he would calling for the glory that is due to the Great Creator...
I plan on dissecting this when I have the time, but could someone please point out where I called anyone names? Or is this persecution complex thing a common trait in these folks?
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