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

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.

24 comments:

Intelligent Designer said...

One of the cool things about Wikipedia is that it can be revised to reflect the results of the most recent research. Consider these quotes from the Junk DNA page:

About 98.5% of the human genome has been designated as "junk" (Oct 9, 2006).

About 97% of the human genome has been designated as "junk" (June 26, 2007).

About 80-90% of the human genome has been designated as "junk" (Dec 4, 2007).

Do I detect a trend here?

Doppelganger said...

Yes - the layman's tendency to use unreliable sources.


I take it that you have no response to my rebuttals of your uninformed bilge regarding junk DNA except for parsing Wikipedia?

No response to your being wrong about DNA 'similarity' numbers? Nothing about how complex a human is and how big a 'program' would really have to be to 'code' it?

No explanation of how a genome really is exactly like software?

Just a dopey observation about changes in a Wikipedia entry?

Pathetic.

Gary said...

Jesus Christ! This guy is a DaveScot Clone without the Tard hat and Cheesy Poofs.

Can we find out if he lives on a houseboat too?

J-Dog

Intelligent Designer said...

It looks like you are right about who coined the phrase "Junk DNA". It's not central to my argument so I won't sweat it.

There is a lot of research going on in this area now. I think we should watch the Wikipedia page on Junk DNA and see if the trend continues. You might even want to become a contributing editor.

Apparently your blog is very popular. Since you linked to mine traffic to it has noticably increased. I am a little disappointed that none of the visitors have read the following entries though: Ten Penny Experiment, Politically Incorrect Stratego Rules and Don't Hurt Yourself.

Doppelganger said...

It looks like you are right about who coined the phrase "Junk DNA". It's not central to my argument so I won't sweat it.


Not central, no, but it is indicative of how much effort you put into understanding the issues.


There is a lot of research going on in this area now. I think we should watch the Wikipedia page on Junk DNA and see if the trend continues.


Wikipedia is nice, but you must know that it can be edited by just about anyone. I would like to see who was doing the edits and what their rationale was.
Personally, I only use Wikipedia to on occasion get some decent links. Because it can be edited by anyone, it is a relatively unreliable source of information (I am aware of the recent study that found it pretty reliable, but I prefer not to take chances. In fact, most depeartments at my University do not allow the use of Wikipedia as a source for written assignments). I prefer to get my information from the primary literature.
Of course, removing 3% of a mouse's noncoding DNA didn't seem to cause any problems for them...


You might even want to become a contributing editor.

Nah - I have enough on my plate.


Apparently your blog is very popular. Since you linked to mine traffic to it has noticably increased.


I don't think it is all that popular. I don't spend a lot of time on it. But if it is, that is good.


I am a little disappointed that none of the visitors have read the following entries though: Ten Penny Experiment, Politically Incorrect Stratego Rules and Don't Hurt Yourself.

I suspect that those that visit your blog via a link from here are more interested in seeing a creationist computer softward guy's rants about evolution than anything else.

Intelligent Designer said...

I have read the research on deleting mouse DNA and I don't think you can necessarily conclude that just because you can delete 3% of DNA with no apparent ill affect that it is junk. I would guesstimate that given a clean software program with no dead code you could delete 20% of the code and still have a program that seems to function just like the original one. This is because a lot of code is designed to handle special situations which may never occur for an individual user during the life of the computer that it is installed on.

Consider the anti-virus software on your computer. During the life of your computer more than 99% of the virus signatures will probably never be utilized. Consequently you could delete the vast majority of those virus signatures and the computer would work exactly the same -- unless it was unlucky enough to encounter one of the viruses matching a deleted virus signature.

Robert Rapier said...

Some things never change, do they Scott? It seems like the worst offenders are always the software/electrical engineer types.

Hope all is well with you. The days are short now in Scotland. Looking forward to flying home for Christmas.

Cheers, Robert

Doppelganger said...

Hi Robert,

Thanks for stopping by.

Have you picked up a set of David Naill pipes yet?

Take care old friend!

Dave Wisker said...

I told you those programmers were prima donnas.

JimV said...

I started out as a computer programmer (on the strength of a couple of undergraduate Fortran courses) and wound up as a mechanical engineer (M.M.E.). After 30+ years designing power turbines, my reaction to the "intelligent Design" thesis is that its proponents don't understand how engineering design works. It is very much an evolutionary process, involving trial and error mutations, horizontal gene transfers (reverse engineering of competitor's designs), and natual selection in a competitive marketplace. Cars and telephones have evolved in our life times. We have better short-term memories for what has worked and what hasn't than "nature", so we do it faster, is all.

I hope this provides at least somewhat of a counter-example to the hypothesis that most engineering/computer-programming types are creationist nuts.

Doppelganger said...

Hi Jimv,

Always a pleasure to get some insights form those in the profession whose minds have not been turned to mush by their religious programming.

But I must say that I don' think that the hypothesis is that 'most' engineer types are creationists. I think it is that when one encounters a creationist, they are more lilely to have an engineering background than, say, a biology background.

I know many engineers that are definitely not creationists. But those that are creationists tend to have an ego the size of Siberia and seem to think that because they are engineers, they have some sort of special insights into biology. See my posting here.

Doppelganger said...

I have read the research on deleting mouse DNA and I don't think you can necessarily conclude that just because you can delete 3% of DNA with no apparent ill affect that it is junk.


And you conclude this premised on your in depth knowledge of genetics and biology, right?


I would guesstimate that given a clean software program with no dead code you could delete 20% of the code and still have a program that seems to function just like the original one.


Gee, guess I was wrong... Because after all, genomes operate EXACTLY like computer programs...


This is because a lot of code is designed to handle special situations which may never occur for an individual user during the life of the computer that it is installed on.



Awesome. So, given your amazing insights into genetics and genomes based on your experience as a computer programmer, what ARE the regions deleted in the mouse knock-outs programmed for? It is not as though you will need to have more knowledge of the situation or do more research - you didn't need any of that to conclude what you have so far!


Consider the anti-virus software on your computer. During the life of your computer more than 99% of the virus signatures will probably never be utilized. Consequently you could delete the vast majority of those virus signatures and the computer would work exactly the same -- unless it was unlucky enough to encounter one of the viruses matching a deleted virus signature.


Wonderful - you have made it oh so clear that genomes are exactly like computer programs.

So tell me - how many computer programs are you aware of in which a coding error makes a few lines of code repeat over and over and it produices a benefit for the system?

Intelligent Designer said...

I have never said or meant to imply that DNA is exactly the same as a computer program. I would assert that DNA is analogous to a computer program and I think you agree with that. My point is that there is more than one hypothesis that can explain the fact that some mouse DNA can be deleted without an observable affect; and I provided one example.

You said: So tell me - how many computer programs are you aware of in which a coding error makes a few lines of code repeat over and over and it produices [sic] a benefit for the system?

I don’t want to put words in your mouth but it appears that your unstated argument goes like this:

If repeated lines of code are found in software they are junk.
DNA is exactly like a computer program. [sic]
Therefore, any repeating sequences found in DNA are junk.

Doppelganger said...

I have never said or meant to imply that DNA is exactly the same as a computer program.


No, of course not...

I guess all those words really mean nothing.


I would assert that DNA is analogous to a computer program and I think you agree with that.


Analogous. Sure. If we use the concept of an analogy the right way. Analogies are but approximations, and in education, especially science education, analogies are useful to convey complex concepts by relating them to everyday ones. But a good educator is quick to point out the limitations of analogies.
Analogies, as much as creationists like to claim they are, are NOT evidence. Analogies are instructional tools. To say that DNA is sort of like a computer program or the english language is fine, providing one realizes that the similarity ends at 'sort of like.' Creationists seem to have a problem recognizing, or maybe accepting,. the limits of analogy. I have, in fact, had more than one creationist insist that analogies are evidence.

Do YOU think analogies are evidence? I mean, the moon sort of looks like swiss cheese...


My point is that there is more than one hypothesis that can explain the fact that some mouse DNA can be deleted without an observable affect; and I provided one example.


No, you provided a non-biological analogy as if it were directly applicable. I think you believe your 'hypothesis' is viable because as you stated, you are a programmer, and you believe DNA is like a program, and that - what was it? Ah yes:

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


No, if researchers started thinking more like software engineers and less
like evolutionary biologists our understanding of genetics would be undergoing its umpteenth revision as the 'bugs' of all the previous 'understandings' were being ironed out...


You said: So tell me - how many computer programs are you aware of in which a coding error makes a few lines of code repeat over and over and it produices [sic] a benefit for the system?

I don’t want to put words in your mouth but it appears that your unstated argument goes like this:

If repeated lines of code are found in software they are junk.
DNA is exactly like a computer program. [sic]
Therefore, any repeating sequences found in DNA are junk.


Yes - better not to try to put words in my mouth.

I am not even discussing junk DNA - I guess this evolutionary biologist left the programmer behind.

No, my question is as stated:


how many computer programs are you aware of in which a coding error makes a few lines of code repeat over and over and it produices [sic] a benefit for the system?


I even left in my typo.
Note I wrote nothing of junk DNA.
I am on the DNA=computer program notion.


And it is funny - depending on which side of the argument to take, creationist with computer programming backgrounds will claim mutually exclusive things in hopes of 'winning.' For example, charlatan and propagandist R. David Pogge claimed that a few lines of code being screwy in a program with millions of lines of code will destroy a computer program (thus all mutations are bad, thus no junk DNA), while one CK Lester claimed that programs can 'lose' or alter up to 30% of their code and not suffer any consequences (thus mutations are no big deal, thus no junk DNA).

Funny thing was, Lester relies on Pogge for most of his anti-evolution claims because Pogge is a software geek like Lester is...

So, what is your position? Do you side with Lester (programs can lose 30% and be fine*) or Pogge (a few lines out of millions destroys the program)?


*this was in response to when I explained the wobble hypothesis to him...

Intelligent Designer said...

I don’t know who Pogge and Lester are but it is obvious to any programmer that both statements about software are true depending on the context in which they were made. Most programs have an initialization section and if a small portion of it gets corrupted the program won’t start. It is also true that many software programs have error handling sections and code sections that support rare cases or minor features. Depending on the application, this could easily be as much as 30% of the code. You could delete those sections of code and the program would function, but it wouldn’t function as well. However, if a person were to use a hex editor and randomly start corrupting an executable it wouldn’t be long before a critical section of code was clobbered and the result would be a fatal error.

Now we both agree that DNA is not exactly the same as software. To say that software and DNA are only analogous is probably too weak of a statement. It is more accurate to state that DNA and software share similarities. I would assert that both software and DNA contain highly ordered and complex information. Would you agree with that? I would also assert that mankind has never engineered any thing nearly as complex as human DNA. Would you agree with that?

Doppelganger said...

More later - but what is so 'complex' about human DNA? Is it more complex than, say, fish DNA? If so, how? And how was the complexity measured?

Intelligent Designer said...

My questions were simple.

Would you agree that human DNA contains highly ordered and complex information?

Would you agree that mankind has never engineered any thing nearly as complex as human DNA (or fish DNA)?

Doppelganger said...

Can you answer these or not?

What is so 'complex' about human DNA? Is it more complex than, say, fish DNA? If so, how? And how was the complexity measured?

Please define your terms, for starters.

And really, DNA as a molecule is not all that complex. It is the post hoc attribution of 'information' that makes it appear so 'awesome' to some.

Doppelganger said...

I don’t know who Pogge and Lester are but it is obvious to any programmer that both statements about software are true depending on the context in which they were made.

And yet they made their claims mutually exclusive. Pogge declared that changing just a few lines of code in millions ouwl be fatal, Lester that 30% is no big deal. Both were made in order to try to prove that mutations must be all bad.

Let me put it more DNA-relevantly:


Can you randomly change evey third bit in a line of code and have a functioning program?

Can you duplicate complete lines of code and increase the functionality of a program? Can you insert short lines of code within programs that make subroutines of the prgram increase their outputs and produce increased functionality of the program?

Most programs have an initialization section and if a small portion of it gets corrupted the program won’t start. It is also true that many software programs have error handling sections and code sections that support rare cases or minor features. Depending on the application, this could easily be as much as 30% of the code. You could delete those sections of code and the program would function, but it wouldn’t function as well. However, if a person were to use a hex editor and randomly start corrupting an executable it wouldn’t be long before a critical section of code was clobbered and the result would be a fatal error.


Makes sense. Pity that more creationists with computer engineering/software engineering backgrounds cannot be as forthright in their explanations.


Now we both agree that DNA is not exactly the same as software.


Good start.



To say that software and DNA are only analogous is probably too weak of a statement. It is more accurate to state that DNA and software share similarities. I would assert that both software and DNA contain highly ordered and complex information. Would you agree with that?

Complex? Depends on the definiton, but I see no problem there. Same with ordered. The problem I see is the use of such terms as "evidence" for design/creation. Our appending of such descriptive terms ot non-human activities/entities does not make them the equivalent of human contrivances. It seems to be common practive to employ this post-hoc reasoning in creationist circles - sure, a genome is "complex" and "ordered" - now - but this does not preclude a less ordered, less complex history.

Intelligent Designer said...

Your questions about software don’t really make sense but I think I know what you mean. For example, there is nothing random about modifying every third bit since a bit can only have a value of 0 or 1. Also one doesn’t modify bits in a line of code. Lines of code are modified with a source code editor which provides a higher level view of the program. Your other questions suffer from similar problems so I can’t really answer them. Nevertheless, I think you are trying to find out if some of the patterns seen in DNA would make sense in a software program. In particular I think your concern is related to repeating sequences in non-coding DNA.

My short answer is “I don’t know”. I haven’t been able to find specific enough information about the nature of these repeating sequences to make a judgment. Does repetition occur in software? Yes. Generally speaking you don’t encounter it at the source code level where you would be talking about lines of code. However, whenever a method or a subroutine is called registers are pushed on the stack; and when they return, registers are popped off the stack. This repetition is not evident at the source code level because it is handled by a compiler. It is evident at the assembly and binary levels. The same could be said of object allocation or other mundane tasks usually performed by code that is generated by a compiler. In short, repetition is readily observed at the binary level but not at the source code level.

Doppelganger said...

Your questions about software don’t really make sense but I think I know what you mean.

Nice 'ad holmium' (LOL!)....

But seriously - now you know how I feel reading your claims re: genetics and biology...


Still no definitions of 'information', 'complexity', etc....

Doppelganger said...

He's going...

He's going....


He's gone!

Too many "ad holmiums", I guess!

LOL!

Intelligent Designer said...

Hi Scott,

I recently published another blog post explaining why repetitive DNA sequences make sense from a design perspective. I haven't got many hits on that post so I am counting on some scathing analysis from you to boost traffic. In return I’ll link back.

Andrew said...

Two questions:
1. If there is a definite number of genomes in the human DNA, (Apparently, it has been 'mapped.') Why is it that no two research groups are coming up with the exact same answers? I've gotten as little as 97.75% similar to chimpanzees to 98.9% similar. Who is 100% correct on this and who miscounted and decided to just make a pretty close guess? I understand FULLY how monotonous counting out 3 billion base-pairs must be, looking for differences... but as highly educated (and paid) as these scientists are, can someone give me the exact correct amount so I can know?
2. It is very nice to know so little DNA is required to have a chimpanzee or a human... depending upon what order the 2.25-1.1% DNA difference is laid out. However, can someone please tell me how much DNA humans have in common with other humans... say a Caucasian with a Philippino? (Please... as exact numbers as scientifically possible.)

Thank you. Wonderful discussions on this site. The name calling is a bit unprofessional, but the sarcasm is great and refreshing. LOVE the comment on the computer guy. LOL! Funny, cause I'm a bit of a computer geek myself.
But don't blame us for being curious about DNA. It truly is amazing stuff!!!

Any RELEVANT answers, please send to a_stombaugh@juno.com. Thanks.