Commentary on the so-called Creation/Evolution/Intelligent Design Debate and Right-Wing nuttery in general - and please ignore the typos (I make lots!)

Wednesday, December 26, 2007

More from "Intelligent Designer"

The Intelligent Designer that I have been discussing here replied to my comment on his blog some time ago and I never read or replied, as I wrote my own post about it (see link). But I finally checked to see if he had replied, and he had.

From here, interspersed with my commentary:

Doppelganger said:
what special insights into genomes and genetics does being a software engineer provide?


I had asked this since Stimpson had indicated that software engineers had some sort of special insight into things that they have no knowledge of, namely, genetics.


I have spent a significant portion of my career working on embedded systems such
as on board flight computers, data acquisition and control instruments and bar
code readers.


But no biology classes? No experience with genetics? Huh... Imagine that...



To design these things software, mechanical and electrical engineers were
required to pool their knowledge to accomplish the task. No one person or group
of persons belonging to only one engineering discipline would be able to
it.


I wouldn't doubt it. This gives you insights into genetics and genomics how again?



In like manner, to untangle the mysteries the human genome, which has a much
grander design than any of the things I have worked on, it will require the
combined knowledge of people with specialized knowledge from several
disciplines.


A couple of issues.... Not understanding everything about the genome does not indicate a 'grand design.' And I am still not sure how not understanding anything about biology/genetics (as Stimpston does) gives anyone special insights into it, regardless of their actual backgrounds. I know engineers can and have contributed ot DNA research, but these were engineers that actually took the time to learn about and understand and gain experience working with DNA, genetics, etc., as opposed to simply believing that BECAUSE they are engineers, they have some special insights and can pontificate on the matter because superficially, genomes seem to act sort of like computer software.



A computer scientist with a grasp of information theory and design patterns
could certainly bring something to the table that a Professor of Biology like
you could not.


Indeed. But such a person would have to understand how to apply their knowledge appropriately, and employing direct analogies and claiming them as evidence simply will not work.



I would wager that it would be easier for a group of biology professors to
design a kidney dialysis machine or a prosthetic hand than to decode the human genome.



What do you mean 'decode'? While there is certainly much to learn, I think you are coming at this with a 1980's mindset (scientifically).


Doppelganger said: How much experinece[sic]/education do software engineers
generally get in the course fo[sic] their educations/careers?

So what’s your point?

I think a few words got cut off their - my point was - how much education/experience in the biological science/genetics does a typical software engineer get. I think it a valid point.

But the Randy saw my blog entry here, and got upset:


On his blog Professor Scott P. [Doppelganger above] criticizes this
blog entry on Junk DNA. His argument includes ad holmium [sic] attacks,
psychoanalysis, insults, misrepresentations, poor logic and some information.


Perhaps, but one will notice that Stimpson did not bother to actually point out any of these supposed transgressions. But let's take a look.

Well, I did write that being a creationist with an engineering background seems to produce some sort of narcissistic psychosis. A bit harsh, I suppose, but how else to describe the notion that simply being an engineer and a creationists gives one some sort of all-powerful insights into things that the person does not actually understand very well? Such folk certainly believe that they are intellectually superior, that much is trivial to document.
I did mention that Stimpson's post on Junk DNA was silly and such, but then I went on to explain why. I did not claim that Stimpson's opinions on the matter are wrong BECAUSE he is an engineer, a creationist, or anything else - no, those are just window dressing. His opinions are wrong because they are wrong.
And sure, I was sarcastic and smarmy. Big deal. I still made my points and had some fun doing it.

Others chime in with condescending remarks. Even Professor Larry Morgan chimes in from his blog to add insult. I try to be nice and stick to the topic of the debate but can’t resist the occasional sic.




I'm sure. And picking on my typos - which I advertise, by the way <Commentary on the so-called Creation/Evolution/Intelligent Design Debate and Right-Wing nuttery in general - and please ignore the typos (I make lots!)) - when you outright misspell something is a bit... silly.

But Randy - who I am sure is a nice fellow - has yet to be able ot support his claims, defend his assertions/position, or show where I have been wrong.

IOW - a creationist.

**ADDENDUM**

Perusing Randy's blog, I found a couple more gems:

"... I think the most commonly believed alternative (evolution by random mutation) is ridiculous. "

No explanation why, of course. But hey - Randy has experience with software engineering, so surely his opinions on evolution are very valid and important...

Monday, December 10, 2007

Are we surprised by this?

I'm not:



W. Thomas Smith., Jr., the controversial web-based reporter who wrote disputed stories from Lebanon, has resigned from his position as a contributor to National Review Online's The Tank blog. Smith had been the subject of a lengthy piece on the Huffington Post raising questions about the accuracy of his
work...


In addition to writing for NRO, Smith, a fomer Marine, is the director the Counterterrorism Research Center at the Family Security Foundation, and the
executive editor of World Defense Review. He co-authored The Complete Idiot's Guide to Understanding Intelligent Design.



Right wing politics, dishonesty, and anti-evolutionism seem to go hand in hand.... in hand...

Sunday, December 02, 2007

Another creationist computer software-type pontificates on things he has no business pontificating on...

So, what is new...

Being a creationist with an engineering/computer programming background seems to produce some odd narcissistic psychosis. These folks just seem to think that they have some special insights into... well, everything. And this fella is no exception.

I was persusing Sandwalk the other day and came across some comments by him, and decided to check out his blog.
I left a few comments there, and instead of just replying to me at the comments section of his blog, or emailing me at the address contained in my blogger profile, he apparently tracked me down and emailed me at my office. That says something right there.

But I came across this blog by him, and it contained so much hubris, ignorance, and sheer nonsense, I just couldn't let it go...

I reproduce the bulk of it here for critique, and will provide commentary where appropriate.


Junk DNA is a myth

Probably one of the most absurd scientific ideas that I have ever read about is the idea that approximately 97% of human DNA is junk. Wikipedia (June 26, 2007) says that:
"About 97% of the human genome has been designated as "junk", including
most sequences within introns and most intergenic DNA. While much of this
sequence may be an evolutionary artifact that serves no present-day purpose,
some is believed to function in ways that are not currently understood.
Moreover, the conservation of some junk DNA over many millions of years of
evolution may imply an essential function."
It's hard for me to believe that any thoughtful person could believe such
an absurd theory.


Ah, the old argument from personal incredulity. The argument from personal incredulity is essentially an argument from ignorance coupled with the arguer's overconfidence in their own powers of comprehension and deduction. As of Dec. 2, 2007, the Wikipedia entry on junk DNA now reads in part:

About 80-90% of the human genome has been designated as "junk", including most sequences within introns and most intergenic DNA. ... Some consider the "junk" label as something of a misnomer, but others consider it apposite [sic] as junk is stored away for possible new uses, rather than thrown out; others prefer the term "noncoding DNA" (although junk DNA often includes transposons that encode proteins with no clear value to their host genome). However it now appears that, although protein-coding DNA makes up barely 2% of the human genome, about 80% of the bases in the genome may be being expressed, which supports the view that the term "junk DNA" may be a misnomer.[1]



But let us see why this software writer thinks that it is absurd that anyone that accepts what the evidence actually indicates...



On what authority do I make such a claim? Well, not much. I am not a geneticist
or a molecular biologist. In fact, I only know slightly more about DNA than the
average college educated person.


Indeed. And this is one of the reasons that people like Randy Stimpson come to the conclusions they do. It is not uncommon for people to draw erroneous conclusions when they do not grasp the issues under discussion. But this is no obstacle for the "Intelligent Designer," Randy Stimpson. He doesn't NEED to understand DNA or genetics of molecular biology. Why? Becuase he writes computer software!



However, as a software developer I have a vague idea of how many bytes of code
is needed to make complex software programs.



Actually, you have an idea about how many bytes of code is needed to make complex computer software programs.



And to think that something as complicated as a human being is encoded in only 3
billion base pairs of DNA is astounding.


It may be astounding, but that's all there is, Jack. This should be the first hint that a genome is NOT, in fact, just like computer software. But no sirree- not to Randy Stimpson, software engineer!



To be more specific, since DNA alphabet consists of 4 nucleobases, we can represent a nucleobase with 2 bits data. This means that 4 base pairs can be represented by a byte of data and approximately 4 million base pairs can be represented by a megabyte of data. This means that the entire human genome can be represented by only 750MB of code. From my experience as a software developer, this would have to be highly efficient code. To suggest that 97% of DNA is junk implies the implausible -- that less than 23MB of DNA is not junk.



Ok.... So this software writer - with no real understadning of genetics or molecular biology, who nevertheless apparently believes that the genome is not just analogous, but the rough equivalent of a computer program - believes that the "code" in the genome must be highly efficient in order to encode something so 'complex' as a human.

So, sit back y'all - an in-depth, verifiable, justifiable, empirically derived series of explanations describing just how complex a human is must be forthcoming, for how silly and truly absurd it would be to declare that a human is so complex that there must not be any junk DNA unless one actually knows just how 'complex' a human is quantitatively...
Right?


By comparison, Microsoft Word has a size of 12MB.I think it's more probable that
the human DNA which we have discovered so far doesn't contain all the
information required to produce humans.


WOW! So there is some 'hidden' secret DNA that darn it - those silly biologists just haven't discovered yet! But wait a sec - how does Randy Stimpson know this? Let's find out - it MUST be coming up!



I wouldn't be suprised if more DNA, or some other kind of information, is
discovered some time in the future.


Oh, right - because you know, us stupid biologists just don't know where to look for extra DNA in cells and such...
But I am still waiting for Randy's explanation for how complex a human is, and what size 'program' would be necessary to code for it... I DO hope this very relevant information will be forthcoming - maybe Randy is just a master showman and will bring it out near the end.... ?



On a historical note, the term "junk DNA" was coined by biologist Roy Britten who once explained junk DNA in this way: "Trash you throw away. Junk you keep in
case it may be useful." This guy is one of the two scientists that "determined"
that human DNA and chimpanzee DNA differ by only about 2%. People who often
quote this so called fact are probably under the impression that this 2% number
is based on some kind of molecue-by-molecue comparison. The number was actually derived by measuring the temperatures at which matching DNA of two species comes apart.

Ah, yes.... Where to start?

No, Randy, Roy Britten did not coin the phrase, it was M. Ohno (at least most attribute it to him). And I can't believe that so clever a creationist software engineer would be so uninformed on what the % similarity figures are all about. I suspect that Stimpson just got that bit of disinformation from Don Batten's "Answers in Genesis" gibberish on the subject, or perhaps from Sarfati's terrible propaganda tome (he 'borrowed' Batten's slop for his book).

Well, here you go "Intelligent Designer" - the REAL story on the percent similarities. No need to reinvent the wheel - I am cut and pasting this from my Amazon.com review of Sarfati's tripe:

***
In reality, the % 'similarity' figures had been batted about for a few years [prior to the Sibley and Ahlquist paper that did employ the techniques alluded to by Randy Stimpson above] - it was the Sibley paper that got quite a bit of attention because
1. DNA-DNA hybridization compares the entire single copy genome
2. Sibley and Ahlquist were accused of fraud because they did not explain the techniques they used in deriving their figures and when others replicated their work, they came up with slightly different numbers.
The original numbers were gleaned from direct DNA sequence comparisons, and, sadly for Sarfati's readers (and Sarfati himself), the numbers have been borne out by ever more studies using many more loci.

Studies pre-dating the S&A paper cited in Sarfati's book:

Chimpanzee Fetal G-gamma and A-gamma Globin Gene Nucleotide Sequences Provide Further Evidence of Gene Conversions in Hominine Evolution.
Slightom et al., 1985Mol Biol Evol 2(5):370-389.
This paper found a 1.4-2.25% nucleotide difference, depending on which sets of alleles are compared.(1.8 kilobases). That is 97.75-98.6% identity.

Primate Eta-Globin DNA and Man's Place Among the Great Apes.
Koop et al., 1986.Nature 319:234-238.
This paper found a 1.7% distance measured by direct comparison of aligned nucleotide sequences (2.2 kilobases in a pseudogene). That is 98.3%.

Just one paper of many post-dating it that come to similar conclusions:

A Molecular View of Primate Supraordinal Relationships from the Analysis of Both Nucleotide and Amino Acid Sequences. Stanhope et al., 1993.
In Primates and Their Relatives in Phylogenetic Perspective. MacPhee, ed.
This book chapter discusses Epsilon globin gene, (~4 kilobases), 1.1%. That is 98.9% identity
***
There are in fact dozens if not hundreds of papers on the topic, all employing direct sequence comparisons. You'd think an "Intelligent Designer" would not be so gullible as to believe everything written by creationist propagandists.

So, no, Randy, the percent figure is not just "derived by measuring the temperatures at which matching DNA of two species comes apart", thoug that is one way to compare essentially the entire genomes of organisms, it is through direct sequence comparisons.


Perhaps if researchers started thinking more like software engineers and less
like evolutionary biologists our understanding of human DNA would grow faster.


Somehow, I doubt it.

Say - where was the "Intelligent Designer's" detailed explanation of the complexity of a human?
Where was his explanation for how many bytes a 'code' should have to produce a complex human? Or is his personal incredulity supposed to convince us all?

Another Salem Hypothesis/Dunning-Kruger data point.