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

Tuesday, February 19, 2008

Software developer PROVES that there is no junkDNA*... and other stuff

Well, the Intelligent Designer is at it again...


In a new post on his blog (see below), he all but declares that there just cannot be any junk DNA in the genome - or well maybe 5%, tops. He further declares that I for some reason 'need' there to be lots of junk DNA, and that when I responded to his silly previous commentary about junk DNA I presented no facts, just insults.

Poor Randy Stimpson, creationist software developer.

He thinks he's got this great analytical mind, but he just didn't get it.
He didn't get that the primary purpose of my post here was not to 'prove' that there is lots of junk DNA, but to prove that a creationist software engineer with minimal understanding of evolution and genetics nonetheless believes that BECAUSE he is a software engineer that he has special insights into what MUST really be in the genome. And, of course, since he KNOWs that there is not much 'junk' in software, there cannot be much junk in DNA. Because after all, DNA is just like software (even though he admitted it isn't).

I also set out to show that you were clueless as to who actually coined the term 'junk DNA' and how % sequence similarities were determined, which I did.

Then, recall, you couldn't actually define "complexity" or how "complex" the human genome should be to 'code' for a human, which was, by the way, one of the linchpins of your argument! But far be it for a creationist with no relevant education, experience, or training (much less understanding of) in the relevant sciences to pontificate on such matters - it is what they do.

Then, Stimpson got all upset because I did not bow down to his software developer supremacy and whined, to which I responded here.
Still no definitions of terms or attempts to justify his claims.
Remember - I had not declared anything specific about junk DNA at all, really, except for the fact that I know that there is some.

So then I commented on his silly blog post about how entropy disproves evolution or some such gunk. He got all in a tizzy about that, too. It was in his entropy post that he declared outright that because he is a software developer, he has some special insights into things having nothing to do with software.

So anyway, Randy went a way after being again unable to support any of his claims and hurling a bunch of false accusations about me using "ad holmiums" and such (the great analytical mind of the creationist software developer diod not bother to try to even learn how to spell "ad hominem", much less find out what it actually means).

And then he tried to write an opus on his own blog, using his amazing engineering insights, to explain how there must be little or no junk DNA in the human genome. So confdent is he that he titles his post Most DNA is not junk. So what else can I do but demolish it?

Here is the relevant portions of it, with my commentary interspersed:



In my blog entry Junk DNA is a Myth I spouted off about how it was ridiculous to think that 97% of our DNA is junk. I could believe 5% junk due to entropy but not 97%. This blog entry came under criticism by Professor Scott P. who seems to have a vested interested in believing in junk DNA. In his criticism, he never provided any proof that the vast majority of DNA is junk, just ridicule. This ridicule may have been a knee-jerk reaction to my blogging alias “Intelligent Designer”.
Actually, my only vested interest is in reality. I do not know the exact amount of truly 'junk' DNA in the genome, but I know it does exist, for I have seen it in my research. As I have indicated - and as my blog posts here pretty clearly indicate - it was not my intent to prove any such thing about junk DNA at all, rather it was to expose the naive manner in which non-biologist, non-geneticist creationists, especially those with engineering/computer backgrounds, attempt to assert their superior authority on all matters (the reader may find it funny that after I had shown Randy how wrong he was on several issues that his recourse was to try to goad me into taking some silly 'IQ' type quiz so that he could 'prove' that he was better at figgerin' stuff out than me because he did pretty well on this quiz).

The ridicule was for your pompous yet error-riddled pontifications and arrogance.

And, of course, you are forgetting the fact that I showed many errors in your claims. Yeah, let's not mention that.



In my defense I am going to make a stab at guesstimating a plausible amount of non-junk DNA in the human genome.
Why re-invent the wheel? Why not look at actual analyses of genomes? Why do you think you 'guesstimates' will be any better than such analyses? Because you are a creationist with a software engineering background? I don't get it.
Here are a few examples of what has been written on the issue:

here
here
here
here
here
here

etc...



I can already hear Scott laughing away in his office now.
You must have very good hearing.



So let’s begin. In this estimate I will be using the word “information” to denote DNA that is not junk and “data” to denote DNA which may or may not be junk. I will also be talking about the data in terms of bytes and MBs [megabytes]. A nucleotide can be represented with two bits of data, a string of 4 nucleotides by a byte of data, and 4 million nucleotides by a MB of data. Thus 3.2 billion base pairs of the human genome is equivalent to 800 MB of data. Professor Page believes the human genome has only 24MB of information and that the rest is junk – that make me laugh.
You may laugh, but that is (more or less) what the actual data indicate. Of course, you have never given a good biological reason why that much 'information' is too little, only reasons that are inapt analogies.



A bacterial genome has 4 million base pairs of DNA and according to Professor Larry Morgan [sic], a bacterial genome doesn’t have junk. So I think it is safe to say that there is at least 1MB of information in the human genome.
Now there are 210 know cell types in the human body. I’ll assume that each cell type requires at least 1MB of information. These cell types share a lot of common features so I’ll assume there is a lot of common information. Just how much of the information is shared between these cell types is a guess. I am going to assume that 90% of the information in each cell type is shared and 10% is unique. This means that 210 cell types require 1MB + 209 * .1MB of information. Rounding this implies that there is at least 22MB of information in the human genome.

That assumption is erroneous. ALL of the "information" is 'shared.' It is a matter of which genes are turned off or on and/or for how long. This is yet another reason why arguments from analogy are largely inapplicable. The genomes of a skin cell and a liver cell are identical (excpet for the odd random mutation incorporated during mitosis). No 'unique' informaiton is in either one, rather, the difference between a liver cell and a skin cell - what makes them what they are - is a matter of which genes are activated and which are not. Skin cells, for example, will have very active genes involved in the making of keratin, while liver cells will not. But a liver cell still has the genes required to make keratin.



But this is just the information needed to construct the different cell types. More information is needed for spatial orientation and to coordinate activity among cells to perform complex functions like vision, motor control, digestion and tissue repair.
Spatial coordination? Whaaa?
Its funny - several years ago, there was a chap on a discussion board - who also had a computer science background - who insisted that each cell had to have encoded in it it's own unique 12-digit grid coordinate so it would know 'where to go.' I asked - repeatedly - if this information changed every time you moved. No reply...
Anyway - this is not an issue that needs addressing, rather, it is an issue of ignorance of development.
Cells DON'T 'know' where to go, because most of them don't actually 'go' anywhere**. The cells that make your hand do not start in one place and 'go' to the hand, the cells are merely 'there' - undifferentiated masses of tissue that are induced to activate and deactivate particular genes at particular times and they become the cells of the different tissues of the hand.
Same goes for 'coordinating' activitities in cells - there is no 'coordination' as such, rather, cells react to various stimuli to produce various outcomes.
It is all too easy to look at a 'finished product' and be in awe ofd its 'completeness', but this post hoc analysis neglects the history and processes involved.



Since the most efficient algorithms to just sort n objects have an order of nlog(n) I am tempted to guesstimate by multiplying 22MB by log(210) to get a lower bound. But that would be bad applied math and just plain lazy. But then again I am not exactly getting paid to do this (wink).
And you are assuming that genetic 'algorithms' are just like those you might employ as a software developer. Why?
Had you even considered the mere possibility that genomes might not really operate just like computer software?



I can think of two other approaches that could be taken. For one of them I need some data points. In particular I need size data about genomes of the simplest multicellular life forms that are well studied and believed not to have junk.
TO BE CONTINUED


Shouldn't you have retrieved such data BEFORE pontificating - laughing - at how much 'information' folks like me supposedly believe are in the genome?
And shouldn't you be able to define "complexity", and be able to produce a viable measurement of the complexity of a human so that you can apply your 'guesstimates' , before any of this other stuff is done? After all, your original claim was that the genome couldn't possibly have enough "information" to encode so "complex" a structure like a human, remember?

-------------------------------------------------------------------------
*Or, at least he plans to...

**a few cell types do migrate during development, such as the cells of the neural crest and the undifferentiated gametes, but these are the excpetion and do not "know" where to migrate to, either - they are 'compelled' to migrate by following chemical gradients.


**ADDENDUM**

Seems PZ Myers didn't dig Stimpson's gibberish, either...

11 comments:

Curtis Forrester said...

"since he KNOWs that there is not much 'junk' in software, there cannot be much junk in DNA"

This guy has positively no idea about how much junk really exists in software - he's obviously not seen the code-base of the software I currently work on. This software is only about 7 years old and already through the natural process of refactoring and (ahem) evolution, produced more redundant, junk code than you'd expect looking at the user-facing aspect of the software. Any software that is older and has been through any amount of rework will contain lots of junk code since it requires more work, testing and risk to remove it. We simply leave it in.

Doppelganger said...

Interesting, Curtis.

Somewhere in this mess of a blog I have written about two other creationist software/programmer types who make diametrically opposing claims regarding 'errors' in computer code. One says even a few errors in millions of lines of code are fatal, the other claims that 30% or more can be altered with no real effect. I guess it depends on which day it is as to which side of the argument a creationist will take.

Thanks for stopping by.

Intelligent Designer said...

Hey Curtis, you are quoting Scott not me. I never said that. Scott isn't very good at representing the point of view of others. He is good at projecting though.

Doppelganger said...

Hi Randy,

I see you have as much problem understanding what "projecting" as you do understanding what "ad hominem" means - after you learned how it was actually spelled.

True, you never said those specific woprds, but how, exactly, is that "projection"?

Are you actually trying to claim that you think there is lots of 'junk DNA' in genomes? That you don't use your 'expertise' as a software engineer as a badge of pseudoauthority on matters having nothing to do with software engineering? If so, then you'd best change a couple of your blogs.

And is this:
"who seems to have a vested interested in believing in junk DNA"
an accurate representation of my position? Of course not. But what do you care? You are a software develpoer and don't accpet evolution, so you must know ALL.

What is of note, of course, is that the creationist had no counter to any of the rebuttals of his claims I provided.

Just whining.

Zeno said...

I believe it is an "ad holmium" attack when one accuses someone else of being "elementary" or perhaps "simple." Sometimes applied to good old Dr. Watson.

Doppelganger said...

Elementary, indeed...

Better, I suppose, than the ad hafnium argument.

Humanistic Jones said...

Way to address this topic! This post plus the response+comments over on PZ's blog have me working on my own analogy for the "data" in DNA. Surprisingly (or not) you can actually get quite a bit of complexity out of the relatively small amount of coding areas of DNA if you take the view of the Development Environment as a Turing Machine in which the base pairs need not actually contain anymore information than the very letter they represent in our designations for them.

Doppelganger said...

HJ,

You seem to have been the only commenter at PZ's that actually got it:

"Boy, humans sure to look complicated and DNA would just be too simple to make a person if there was Junk DNA. I can't think of any way that a small amount of DNA could ever make a whole person... therefor goddidit!"

The comments have been interesting, but I haven't really seen any that address the core of Stimpon's blunders (except for PZ's actual blogging).

Intelligent Designer said...

Hey Scott,

Why don't you go over and read HJs blog entry Better Thought Out Look At DNA As Data and tell us what you think of it.

HJ,

Can you enable comments on your blog, I would like to respond. I promise to be nice.

Curtis Forrester said...

So, Zeno ya made me laugh real good.

@Randy - I really don't feel that software and DNA are analogous. Software is a rigid set of steps, event handlers and data structures. While DNA might correlate to an in memory data structure from an information standpoint data is fully passive. Everything in biology seems to have both an information and a behavioral aspect to it. It's physics. Data just sits there until something reads or mutates it. Lipids behave like they do because of physics.

I do think, however, that software that is newly designed/written looks very different when compare to code that's been around awhile, and this illustrates what we're hearing about DNA and so-called "junk" information in it. Newly designed software that's well planned out is highly efficient and there is very little that is redundant and not used. This is what is expected with something that is specifically designed.

The other scenario is with software that has been around awhile - especially when pieces are reused. We often will reuse whole sets of classes that were originally designed for something totally different, but there is just one feature that we need from it. Rather than strip out all the unnecessary parts we include the whole but only use what we need. At any time we could use other parts of the code should the situation require it.

The situation is also a bit easier with software. It says, Copyright 2007 Acme. I don't think they've yet found a watermark in DNA that says "Copyright (c) 4004BC God. All rights reserved."

Anyway, good conversation.

Humanistic Jones said...

ID

Dang, I thought they were enabled... derp on my part! I kinda wondered why no one had taken to this.