The Complete Idiot's Guide to Intelligent Design

Posted 19 January 2005 by PZ Myers

Adam Felbers has a hilarious take on the ID movement, a Q&A on the theory of Intelligent Design:

Q: So what is ID doing to research the identity and characteristics of this "intelligence" that it posits?
A: Well, nothing that I've found yet...

Q: Because if they really wanted to research stuff, they'd be saying things like, "Well, could a giant lobster make a flower?" and, "Is there anything about the design of DNA that looks like something a space crustacean would come up with?"
A: I really think you need to get off this whole lobster thing.

Q: But these ID guys aren't looking into just who this intelligence is, are they?
A: No.

Q: Because they think it's God, right?
A: They don't say that.

Q: Because if they thought they saw evidence of giant superintelligent eyestalks peering down on them from under a celestial carapace, they'd be seriously bummed, wouldn't they?
A: I think this Q&A is over now.

It's funny because it is so, so true.

39 Comments

DaveScot · 19 January 2005

Could a lobster make a flower?

I dunno. But I bet an amoeba dubia could.

http://www.cbs.dtu.dk/databases/DOGS/abbr_table.bysize.txt

I was idly contemplating the notion of a LUCA with an extremely complex genome that was more or less a superset of everything that has come along since so out of curiosity I wondered what organism (so far) was known to have the largest genome. Imagine my surprise when I discovered that ameoba dubia holds the record with 670 billion base pairs (compare to human genome of 3 billion base pairs).

A very complex universal ancestor that reconfigures itself into different forms for different environments using a subset of its genome would obey the second law of thermodynamics (information entropy, not heat entropy). Aside from obeying the laws of physics as applies to information science this also addresses a number of problems with mutation/selection like the rapid emergence of new species and especially the rapid emergence of new phyla as in the Cambrian explosion. It also explains why once a kind is established (fish, bird, mammal, etc.) it remains that kind (fish, bird, mammal, etc.) forever after regardless of how much time passes for mutation/selection to turn it into something different. It remains that kind because the genomic information for different kinds is no longer a part of it and the law of information entropy requires that once the information is gone it cannot be regained.

This of course begs the question of where the LUCA came from and that may be an exceedingly difficult question but that's the breaks, folks. As Plato said "follow the evidence, wherever it leads". The evidence and natural law points to life on earth starting with a complex LUCA that has evolved into simpler forms to fit a changing environment.

Jim Harrison · 19 January 2005

Prokaryotes appear in the fossil record long before eukaryotes. Prokaryotes have very small genomes relative to eukaryotes. Somehow the genomes got bigger.

Next question.

Russell · 19 January 2005

Couple more quotes from the cited website that also bear repeating because they are so very true:

Q: Furthermore, is this not an idea that exists to negate, forcing evolutionary theorists to prove that each and every natural phenomenon was NOT created by an intelligence? A: Well... Q: Whereas a real science would not just employ scientific methods to shore up a foregone conclusion, but rather use scientific methods to determine precisely how something operates, right? A: It's science, all right? It's science.

Steve Reuland · 19 January 2005

Imagine my surprise when I discovered that ameoba dubia holds the record with 670 billion base pairs (compare to human genome of 3 billion base pairs).

As stated already, prokaryotes existed long before any eukaryotes, and are clearly basal. You seem to have missed a few of the basics. And I'm sure that if you look into your ameoba, you'll find that it's highly polyploid, meaning that it's genome simply consists of a smaller genome duplicated many times over. (Or alternatively, it has a very large number of repeats, probably due to retrotransposition.)

A very complex universal ancestor that reconfigures itself into different forms for different environments using a subset of its genome would obey the second law of thermodynamics (information entropy, not heat entropy).

Sure it would, but so too would a genome expanding via gene duplication and selection, which does not violate the second law of anything. And better yet, it accords with the evidence.

It also explains why once a kind is established (fish, bird, mammal, etc.) it remains that kind (fish, bird, mammal, etc.) forever after regardless of how much time passes for mutation/selection to turn it into something different.

This is the old typological fallacy beloved of creationists. Unfortunately, there is no such thing as a "kind" -- it is not a term or concept that biologists recognize as valid. There are plenty of extinct species (therapsids, for example) which cannot be assigned to any one "kind" except for by way of cladistics, because they are transitional.

The evidence and natural law points to life on earth starting with a complex LUCA that has evolved into simpler forms to fit a changing environment.

The evidence clearly shows that genomes have expanded over time via duplication. And the idea that a single ameoba is more complex than all multicellular eukaryotes put together is just plain nutty.

Jim Harrison · 19 January 2005

Not to turn DaveScot into a merely adorable mascot, but it was kinda charming when he managed to channel various 19th Century biologists by putting ameobas at the root of the tree of life. He should have mentioned a different species than Amoeba dubia, though. Amoeba proteus more adequately evokes the romantic philosophy that lurks behind his obsolete biology because in Greek mythology Proteus was the God who could become anything.

Even as a kid, I couldn't buy into the idea that amoebas are somehow uniquely primitive. Human beings have built transports that move by oar, screw, sail, wheel; and jet; but contriving motion by psuedopodia remains damned hard from an engineering point of view. Amoebas may be one-celled, but they are complex and highly adapted to their lifestyles.

Great White Wonder · 19 January 2005

Dave Springer writes

Could a lobster make a flower? I dunno.

This is the kind of skepticism most people do not brag about, but holocaust deniers are proud of.

DaveScot · 19 January 2005

The C-value paradox.

Now see, if they'd teach the weaknesses of neo-Darwinism I wouldn't be discovering the C-value paradox at this late date. If I wasn't so damn curious and open minded as to question neo-Darwinism I wouldn't have happened across the c-value paradox. In point of fact the more reading one does about genetic evolutoin the more problems one runs into with the mutation/selection theory that attempts to explain it all.

Could someone point me to the fossil record of the first amoeba? I was under the impression they didn't fossilize very well so I have no bloody idea how one can state when they first appeared in the "fossil record".

DaveScot · 19 January 2005

Jim says "kinda charming when he managed to channel various 19th Century biologists by putting ameobas at the root of the tree of life"

Yeah but I put 'em there because of high potential for genome complexity whereas the 19th century dudes put 'em there because they appeared to be the simple blobs of jelly in primitive microscopes.

So far I don't care for any of the theories I've read to account for the c-value paradox which are mostly derived from some theory about junk DNA. The problem with that is DNA replication is a very expensive item in the cellular energy budget. It takes two orders of magnitude more energy for an amoeba to dup its DNA than for a human cell. Fitness demands an explanation for why all the energy is spent. Duplication of useless trash at such a high energy cost is a poor answer. Preserving a library of information that might be needed in the future is a good answer. For instance, if a big enough asteroid hits the earth and makes a new asteroid belt one of the few things that might survive is spores from an amoeba and if those spores contain all the information needed to make everything from trees to the dogs that piss on them well than that makes good sense.

It does however make it far more difficult to accept the proposition that a library containing all the complexity required to build everything from viruses to human evolved accidently in a primordial soup with only 500 million years and no proof testing of the instructions. It probably means that the first cell came to the earth from somewhere else and all the information in its DNA library was tested somewhere else.

Only by allowing the possibility of purpose and design can these possibilities be contemplated.

Before I go searching - has anyone or any group tried developing genome compression algorithms that measure the amount of information entropy in fully sequenced genomes? That would provide a valuable clue in exploring the c-value paradox - for instance if a sequenced amoeba genome could be compressed by a margin far larger than a human genome it would be a good indicator of how much is really junk and how much isn't.

Offhand, from a cursory glance at the c-values for different organisms, it would be reasonable to try correlating potential for morphologic diversity to size of genome. Has anyone bothered plotting c-values into an evolutionary tree?

Steve Reuland · 19 January 2005

Now see, if they'd teach the weaknesses of neo-Darwinism I wouldn't be discovering the C-value paradox at this late date.
— DaveScot

You mean, if you had bothered to educate yourself on the basics of biology, then you wouldn't be discovering the C-value paradox at this late date. Every introductory textbook I've ever seen discusses it, without requiring any phony "weaknesses" of neo-Darwinism to be added in.

If I wasn't so damn curious and open minded as to question neo-Darwinism I wouldn't have happened across the c-value paradox.

That's a pretty sad. It's sort of like congratulating yourself for having discovered atoms, in spite of those dogmatic chemists. Give yourself a gold star.

In point of fact the more reading one does about genetic evolutoin the more problems one runs into with the mutation/selection theory that attempts to explain it all.

So what you're saying is that previously, before having looked into the basics of genetics (and discovering highschool stuff like the C-value paradox), you didn't know what you were talking about at all. But for some reason that didn't stop you from coming here with your mind made up already. And now you toss out a bald assertion with no examples or supporting details. Please quit wasting our bandwidth.

Great White Wonder · 19 January 2005

Fun with Google "David Scott Springer" "liar" "David Scott Springer" "stupid" Keep it up, Springer, you dissembling clown. Why one would wish to develop a public reputation as an obnoxious troll is beyond me.

Could someone point me to the fossil record of the first amoeba? I was under the impression they didn't fossilize very well so I have no bloody idea how one can state when they first appeared in the "fossil record".

Try google, now that you know how it works.

PZ Myers · 19 January 2005

Now see, if they'd teach the weaknesses of neo-Darwinism I wouldn't be discovering the C-value paradox at this late date.

I first learned about the c-value paradox in an undergraduate cell biology course in the mid-1970s. It has been the subject of many papers and a few books since then. Your ignorance of something that has been openly discussed and studied by biologists is not a strike against evolutionary biology. It is also not a "weakness" of evolutionary biology. It's a fact about organisms. The big things it argues against are 1) progressive change in evolution, where there is a hierarchy of complexity that corresponds to particular lines of descent, and 2) and simplistic correspondence between the length of DNA and the complexity of the tissues of the organism. Neither are elements of neo-Darwinian theory, and I'd say that (1), if it were true, would be evidence against our current ideas about how evolution works.

Steve Reuland · 19 January 2005

The problem with that is DNA replication is a very expensive item in the cellular energy budget.
— DaveScot

Not for eukaryotes. It's mostly insignificant. DNA replication is nothing compared to protein synthesis, or -- somewhat relevant here -- motility.

Preserving a library of information that might be needed in the future is a good answer. For instance, if a big enough asteroid hits the earth and makes a new asteroid belt one of the few things that might survive is spores from an amoeba and if those spores contain all the information needed to make everything from trees to the dogs that piss on them well than that makes good sense.

And I suppose those genes just sat around for a few hundred million years, in the complete absence of selection, somehow never mutating? Genes which are not expressed or not under selection will not last forever, they will become pseudogenes. We've got lots of them. If you'll notice, you rejected the idea that cells carry lots of junk DNA on the (incorrect) assumption that it costs too much to replicate it. However, you're saying here that cells carried lots of functional genes that weren't expressed at all, and somehow never got deleted. Isn't that a bit contradictory?

Great White Wonder · 19 January 2005

David Springer, who always wanted to be just like Corwainer Smith, writes

It probably means that the first cell came to the earth from somewhere else and all the information in its DNA library was tested somewhere else. Only by allowing the possibility of purpose and design can these possibilities be contemplated.

Let me get this straight: bears who were too sick to find food in the fall are tested by mysterious alien beings during the winter to see if they should be allowed to survive. Man, that's one stupid theory, Dave. What are the mysterious alien beings trying to accomplish, in your humble opinion?

Steve Reuland · 19 January 2005

Keep it up, Springer, you dissembling clown. Why one would wish to develop a public reputation as an obnoxious troll is beyond me.
— GWW

Look, I know I can be an asshole too, but this sort of rhetoric is really unecessary.

Gav · 19 January 2005

It's late. I like amoebas. Are they a kind of organism, or more of a lifestyle?

Great White Wonder · 19 January 2005

Someone said a dirty word.

Frank J · 19 January 2005

I dunno. But I bet an amoeba dubia could.
— DaveScot

C'mon. Do I have to be the one to say it? As in "don't you mean amoeba dubya?" And yes, I am a Republican. But no politician is sacred.

DaveScot · 19 January 2005

It doesn't make sense on a survival of the fittest POV to carry the overhead of junk DNA. It doesn't make sense to carry any burden that isn't strictly required for reproductive success. Nature doesn't care if any or all life ends tomorrow or a trillion years from now. It's all about a selfish gene. Or so Dawkins would have you believe. There are all sorts of problems that come up when purpose and design are assumed away at the beginning. If one assumes purpose and design are a possibility then elegant explanations become evident. Rapid speciation - no problem - in the absence of a requirement for serendiptous beneficial mutations to accumulate over geologic timespans contrary to law of information entropy, if one assumes that the evolutionary record we see began from a template library of morphologic solutions to anticipated problems, then rapid speciation is easy to account for - all the necessary information was already in the genome and it's a much simpler manner of expression rather than fortuituous creation. Weird c-values that have no correlation to expressed complexity of the organism - no problem - some organisms have a larger measure of the original template library and hence a greater ability to adapt to an environment changing so rapidly it's catastrophic for other organisms. The template library, which is an unneeded burden for the selfish gene that only cares about whether it can reproduce in the next hour or next year, becomes a huge asset for guaranteeing that life continues for millions and billions of years. Indeed, the morphology that leads to the emergent quality of intelligence and tool use might have been an anticipated need for life to continue after the earth becomes a cinder because not even an amoeba spore is going to survive when the sun turns the inner solar system into a giant autoclave.

Now back to the c-value paradox.

Not much progress has been made on the c-value paradox since the mid-1970s it seems. You evolution boys kinda stalled out on a lot of the gaps while I was preoccupied inventing the technology in the computers we're using to talk about it today. But hey, at least you managed to take a page from geology to figure out that the 1953 Miller-Urey experiment was based on bogus assumptions. That's progress, I guess...

Here's some interesting reading on genomic compression by a young Dr. David Krakauer (Oxford 1995 PhD in Evolutionary Theory, now working at Princeton) whose research interests "lies at the interface of evolutionary biology, applied mathematics and computer science". Good stuff. He's a little weak on the computer science side of things but he's got some good ideas. He's tending to want to take what he knows about genetic evolution and apply it to computers. I don't think that's going to be very fruitful. Computers are already evolving millions of times faster than anything biological. I think the more practical track is to take what we've learned from the artifical evolution of computers and apply it to biological evolution in search of answers to some of the more intractible questions.

Anyhow, here's an interesting paper he wrote on genomic compression. It's about varying c-values and natural genomic compresssion like overlapped reading frames, whereas I was really looking for artifical genomic compression algorithm to compare c-value relative to information entropy, but it's all I found so far looking for anything anyone has done on genome compression.

http://www.santafe.edu/research/publications/wpabstract/200205021

Just for kicks, I wonder how well pkzip works on a fully sequenced genome. Somebody must've tried that at least for the obvious archival reasons. You should get at least a 4:1 compression ratio for going from 8-bit ascii encoding to 2-bit ACTG encoding. After that it gets more interesting. Pkzip (tweaked LZW algorithm as I recall) isn't optimized for idiosyncracies in genome strings but it should still pick up some gains.

Great White Wonder · 19 January 2005

DaveScot, outdoing himself, writes

Not much progress has been made on the c-value paradox since the mid-1970s it seems. You evolution boys kinda stalled out on a lot of the gaps while I was preoccupied inventing the technology in the computers we're using to talk about it today.

What was that invention again? The restart button?

Indeed, the morphology that leads to the emergent quality of intelligence and tool use might have been an anticipated need for life to continue after the earth becomes a cinder because not even an amoeba spore is going to survive when the sun turns the inner solar system into a giant autoclave.

But remember Dave that the aliens most likely just want to use the charred earth as a Gorbloppo Ball for the Trans Universal Olympics which occurs every 5 billion years. The tradition of using only planets that have been seasoned with a few billion years of organic life goes back to the Fourth MegaDynasty of Arfoo-Ploink. So there is no need for life to contiue after the sun explodes. In fact, no sane alien wants to touch a Gorbloppo Ball that hasn't been sterilized! I mean, that's just sick, Dave, is what it is.

It doesn't make sense to carry any burden that isn't strictly required for reproductive success.

Is that why you cut your nipples off?

Steve Reuland · 19 January 2005

It doesn't make sense on a survival of the fittest POV to carry the overhead of junk DNA. It doesn't make sense to carry any burden that isn't strictly required for reproductive success. Nature doesn't care if any or all life ends tomorrow or a trillion years from now. It's all about a selfish gene. Or so Dawkins would have you believe.
— DaveScot

If you knew much about evolutionary thought, you'd know that this kind of "pan-selectionist" point of view isn't held in very high regard. Lots of things are subject to selection, but not everything. Things can indeed accumulate that are not required or helpful for reproductive success, as is obvious with much of our non-coding DNA. Viruses in our genome need not have any other "purpose" other than the fact that they were able to replicate, and there they are.

There are all sorts of problems that come up when purpose and design are assumed away at the beginning.

But you see, the view of pan-selectionists is that nothing is without purpose or design. They take all features of living things to be the products of natural selection, which must therefore serve the purpose of survival and reproduction. I don't know where IDists get the silly idea that Darwinian theory ascribes no purpose, or telos, to biological features, but it's a sad case of missing the entire point. Non-selectionist views, however, acknowledge that not everything has a "purpose" in the sense of being beneficial to the organism. Plenty of mechanisms exist to create non-beneficial changes in DNA, such as neutral drift or the expansion of transposable elements. Most evolutionary biologists are neither pan-selectionists nor non-selectionists, they take a middle view.

If one assumes purpose and design are a possibility then elegant explanations become evident.

Such as what? The only explanation you've offerred for the C-value paradox is neither elegant nor remotely plausible.

Not much progress has been made on the c-value paradox since the mid-1970s it seems.

This is quite an ignorant statement. You can read a lengthy review here (pdf) and note that the vast majority of citations are well after the 70s. Almost all progress has been made since the mid 70s.

You evolution boys kinda stalled out on a lot of the gaps while I was preoccupied inventing the technology in the computers we're using to talk about it today.

I can promise you, this kind of haughty attitude -- especially given the ignorance that accompanies it -- doesn't impress anyone.

DaveScot · 19 January 2005

Great White Hope manages to peck out:

Fun with Google "David Scott Springer" "liar" "David Scott Springer" "stupid"

For even more fun substitute "George W. Bush" for "David Scott Springer". Being called stupid and liar by insignificant anonymous twits like Great White Hope doesn't seem to limit one's possibilities. People just consider the source and you are nobody. I understand why you don't let anyone know your name. If I were you I wouldn't either. ROFLMAO!

Wesley R. Elsberry · 19 January 2005

It's about varying c-values and natural genomic compresssion like overlapped reading frames, whereas I was really looking for artifical genomic compression algorithm to compare c-value relative to information entropy, but it's all I found so far looking for anything anyone has done on genome compression.
— DaveScot

Some of the stuff DaveScot didn't find.

Wesley R. Elsberry · 19 January 2005

I should note that in Elsberry and Shallit 2003 we cite six sources concerning compression of DNA sequences:

For example, consider Dembski's claims about DNA. He implies that DNA has CSI [19, p. 151], but this is in contradiction to his implication that CSI can be equated with highly-compressible strings [19, p. 144]. In fact, compression of DNA is a lively research area. Despite the best efforts of researchers, only minimal compression has been achieved [36, 84, 12, 56, 2, 59]. Elsberry and Shallit 2003

Great White Wonder · 19 January 2005

DaveScot again

I think the more practical track is to take what we've learned from the artifical evolution of computers and apply it to biological evolution in search of answers to some of the more intractible questions.

I seem to recall that one of the answers we confirmed using artificial evolution in silico is that relatively complex virtual organisms arise when simple virtual organisms which reproduce imperfectly are subjected to selective pressure. Did I misinterpret that data? That's a little different from what Dave is proposing. Which intractable question specifically do you propose to answer by examining the "artificial evolution" of computers, Dave? And specifically what aspect of the "artificial evolution" of computers do you find relevant to addressing the "intractable question"? Let me know if these are not reasonable follow up questions. We're always happy here to help you 150+ IQ guys sort out your brilliant thoughts from the annoying creationist crudola. For whatever reason, you ID apologists love to "refine" your "theories" this way (funny that there just aren't enough creationist blogs which offer this sort of service).

Great White Wonder · 19 January 2005

DaveScot

Being called stupid and liar by insignificant anonymous twits like Great White Hope doesn't seem to limit one's possibilities.

True enough. Of course, any reasonable person who reads through the comments here will understand that I'm not the only one here who thinks that you're a few marbles short of full bag and less from honest. I'm just one of the few that's crazy enough to think that underneath that thick pink skin of yours is a decent human being that might wake up if he's slapped hard enough.

Tim Brandt · 19 January 2005

Just a quick question - why do you guys respond to Dave Scott? I know reading his bullshit is extremely entertaining, but is it really worth the effort and frustration to answer every one of his insults and unsupported claims? I mean, he invented the modern computer, for Pete's sake! And we will all look back in 200 years and wonder why we hadn't seen all of these grevious paradoxes in evolution centuries before, and wish that we had only listened to Dave Scott. Relax guys, and enjoy the show.

DaveScot · 19 January 2005

Steve, Dawkins isn't held in high regard? Interesting. What's it take to earn high regard in your book, a Nobel prize? Just because you don't understand the function of any given bit of DNA doesn't make it not required for reproductive success anymore than not knowing the roadmap for abiogenesis makes the first living thing a product of divine creation. I'm surprised you'd use the same logic the Discovery crowd uses. Well maybe I shouldn't be surprised since you're all scientists. Maybe scientists and engineers are different species... Since you insist I'm missing the entire point of evolution please tell me what you think the point is. Frankly I think it's you that's lost the plot, not me. So how much of the amoeba dubia genome is non-functional junk? You speak as if you know the answer without a doubt. You must have completely sequenced it, figured out what each bit of it does, and kept it a secret. Your link to the "progress" made since 1970s in understanding C-value paradox starts out with

both the origins and reasons for the clearly non-random distribution of this variation remain unclear. Several theories have been proposed to explain this 'C-value enigma' (heretofore known as the 'C-value paradox'), each of which can be described as either a 'mutation pressure' or 'optimal DNA' theory. Mutation pressure theories consider the large portion of non-coding DNA in eukaryotic genomes as either 'junk' or ' selfish ' DNA and are important primarily in considerations of the origin of secondary DNA. Optimal DNA theories differ from mutation pressure theories by emphasizing the strong link between DNA content and cell and nuclear volumes.

It was unclear in the 1970's and it remains unclear today. What progress has been made - a few obvious theories with no consensus versus no theories with no consensus? That's not progress in my book. I said at the start that the theories were mostly based on junk DNA. Like that's a tough one to come up with. Duh. Equally obvious is selection pressure to make it smaller. Duh again. I already explained that there's a high energy cost associated with DNA replication which you pooh-poohed out of hand so I guess you're aligning yourself the "it's all just junk" theory. My explanation for c-value is not remotely plausible, eh. Which god of truth died and made you the arbiter of plausibility? It's completely plausible if you don't rule out the possibility of purpose and design. Robust designs anticipate problems. That's the benefit of planning. Nature doesn't plan ahead. Nature is REactive. Intelligent design is PROactive. If there's anything in the genome of any organism that's anticipatory of a problem that has not happened to that organism in the course of time it's evidence of design. The more complex and the more numerous the solutions to anticipated problems the stronger evidence. Accumulated mutations addressing a big problem ahead of time by sheer accident is bloody unlikely. Unfortunately for everyone DNA doesn't fossilize so we can only guess about the characteristics of ancient genomes. Technically, according to y'all who object to ID because it makes no falsifiable predictions, that makes ANY theories about ancient DNA not falsifiable so it should all be deposited in the pseudo-science receptacle... fortunately most people don't insist on such a strict standard but it sucks when there's a double standard - one for neo-Darwinism and a different one for anything critical of it.

DaveScot · 19 January 2005

Great White Wonder writes:

I'm just one of the few that's crazy enough to think that underneath that thick pink skin of yours is a decent human being that might wake up if he's slapped hard enough.

I been slapped by far better than you. Tim

why do you guys respond to Dave Scott?

Among my many talents is knowing how to push the buttons that make people respond. The core principle is self-aggrandizement. Everyone wants to put a braggart in his place. All you need is a skin impervious to the inevitable flamage from tools like Great White and/or certain kind of pyromaniacal glee obtained by watching him burn. The remainder is often instructive.

I mean, he invented the modern computer, for Pete's sake!

That's right. And if Al Gore hadn't said it first I'd lay claim to inventing the internet too!

DaveScot · 19 January 2005

Wesley,

Thank you. I hadn't put much time into the search and I have to stop and read what I do find as I go. I made it to the RepeatMasker but was disappointed in that it was library based on a list of mammalian genes and known short sequences, worked only on short subsets, and had few sequenced examples. A lot of the other stuff I found was based on rolling window compression (frame start overlap I think the bioinformatics guys called it) used mostly by viruses and bacteria (where size REALLY counts) to compact their code. Since coding genes are such a small part of most of the big c-value genomes frame overlay of protein coding genes isn't going to be significant as far as compression.

Ya gotta admit, there ain't much there even adding what you found. The authors of one tried pkzip and after the 4:1 compression I said would be the minimum it actually EXPANDED the file size instead of compressing it. That's a friggin' difficult trick to make PKZIP produce a bigger file. It means that the very minimal library overhead (PKZIP assembles a customized library on the fly) is larger than the excess entropy.
Of course as I mentioned LZW is a general purpose compressor and better results can be obtained by tweaking for certain types of redundancies known in advance to be resident in certain types of data sets. I wrote some real-time voice compression software a dozen years ago (the challenge was doing it on the fly with a limited amount of CPU bandwidth) and spent a long time staring at digitized voice prints looking for compressible patterns that couldn't be discerned by general purpose compression algorithms or were too computationally-intensive for my application. There's a LOT of money in the smallest improvments in voice compression - imagine how much money AT&T saves with a 0.1% improvement in compression - it seems small but multiplied by the untold billions of dollars in their voice switching capacity it's BIG money. But I digress...

The other problem with DNA sequence compression is the limited number of fully sequenced genomes they have to work with. Most of the fully sequenced genomes are tiny c-values - bacteria and viruses. These are presumably already highly compressed for reasons practical to the organism itself. Good sized ones like h.sapiens fully sequenced are as rare as hen's teeth for reasons practical to the budgets of the organisms manning the gene sequencing machines.

RepeatMasker however compressed the human genome by some 50% but it's really highly tailored to human DNA. Individual tailoring to other organisms like lillies and amoebas with genomes orders of magnitude larger than humans isn't practical and probably not even relevant. And how long it will be before we even have those genomes sequenced so compression can be attempted might be a very long time.

The most recent DNA tweaked program (not optimized with a mammalian library like RepeatMasker) I noted from your link

http://bioinformatics.oupjournals.org/cgi/reprint/18/12/1696.REMOVEpdf

obtained only marginally better compression than basic LZW. But again, they're not taking a gigantic sequence like amoeba dubia either.

Now I'm off to search for a plot of c-values on an evolutionary tree. I don't know the method of obtaining a c-value (I'd guess it's isolate the DNA and simply weigh it) but there's a lot more of them to work with than fully sequenced genomes. Surely someone has tried looking at them plotted onto an evolutionary tree to see if any patterns are evident...

DaveScot · 19 January 2005

Questions for you dudes what gots all the answers:

What stretch of human dna accounts for a newborn:

1) opening its eyes when awake
2) closing its eyes to sleep
3) crying when it is hungry
4) cooing when it is comfortable
5) knowing how to coordinate all muscles used in nursing

I gots a suggestion for yas. It probably isn't in the few percent of the genome that contains DNA that codes for proteins or the surrounding areas that control gene expression.

Now unless y'all want to embrace the idea that complex instinctive behaviors are imparted when the great bearded thunderer blesses newborns of all sorts with a soul I'd guess that somewhere in the DNA is a vast amount of information for which you don't have clue #1 about.

So please, in the future, when discussing junk DNA, please don't make me laugh by pretending you know more than a tiny fraction of what's really going on there. Saying you can see the tip of the iceberg is a vast overestimate.

So did you guys ever hear the joke about the pig farmer and the monkey?

There was once a pig farmer with a pet monkey. The farmer wanted to win the livestock show by having the largest pig. So he figured if he put a cork in the pig's ass it would quickly bloat up to monumental proportions. But, being a forward looking guy, he knew he'd need to remove the cork after the show. So he trained his monkey to pull corks out of bottles. In a few weeks the monkey was a cork-pulling fool. The monkey made cork pulling motions even when there were no corks around. The farmer won the show with the biggest pig anyone'd ever seen. Upon returning he set about emptying the pig. He got a good distance away and let the monkey go. The monkey, which was so motivated and well trained he was making cork pulling motions constantly, walked over and did his thing. The sh*t flew everywhere, even covering the farmer. When the dust settled the farmer was rolling on the ground laughing. A neighbor, who'd watched the whole affair, walked over and said "You're covered in pig sh*t. What's so darn funny about that?". The farmer, laughing so hard he was crying, said "You should have seen that monkey trying to put the cork back in."

The pig reminds me of Darwin's "black box", the simple blob of protoplasmic jelly he thought was the cell. The black box that didn't get opened for a hundred years after "Origin of Species" was published. The cork is the lid on the box. The creationists are the farmer. The sh*t is the complexity of the living cell. I'll leave it to y'all to guess who the monkey reminds me of...

LOL!

Great White Wonder · 20 January 2005

I think I heard Jerry Don Bauer calling for Dave.

Ed Darrell · 20 January 2005

Unfortunately for everyone DNA doesn't fossilize . . .

Alas, brains and arguments too often do.

Ed Darrell · 20 January 2005

The pig reminds me of Darwin's "black box", the simple blob of protoplasmic jelly he thought was the cell. The black box that didn't get opened for a hundred years after "Origin of Species" was published. The cork is the lid on the box. The creationists are the farmer. The sh*t is the complexity of the living cell. I'll leave it to y'all to guess who the monkey reminds me of . . .

Odd. I'd think the creationists who struggle to deny the pipeline of information are closer to the monkey. It's not science, after all, who is trying to stuff the cork back into anything. Since Tennessee's legislature acted early in 1925, more than 100 times creationists and IDists have asked legislatures and school boards and courts to ban, water down, or subvert the teaching of science. In that time no scientist has ever asked a legal body to ban creationism. There's a moral there, Dave. When life's processes reveal themselves, it's futile to deny them. Those who do try to deny them end up just covering everything in fecal material -- just like your monkey. And make no mistake about it: It is your monkey.

Steve Reuland · 20 January 2005

Dawkins isn't held in high regard? Interesting.
— DaveScot

No, it's your charicature of Dawkins as a pan-selectionist (which he's not) that isn't held in high regard. I think you have a serious reading comprehension problem.

Just because you don't understand the function of any given bit of DNA doesn't make it not required for reproductive success anymore than not knowing the roadmap for abiogenesis makes the first living thing a product of divine creation.

Not knowing the function is not the evidence we have for non-functionality. The evidence is in deletion experiments which remove DNA without consequence, and more importantly, in polymorphisms between individuals within populations that create different amounts of DNA. For example, a polyploid plant which arises in a population now has twice as much DNA. Obviously, it doesn't need that extra DNA if its conspecifics were getting along fine without it. Indeed, the C-value paradox is one reason why we know that all DNA isn't functional, because closely related species can differ markedly in genome size even though they're not phenotypically very different. A lot of DNA inserts itself in the genome through known mechanisms. In many cases (though not all) this insertion is completely random. Sometimes, it causes nasty diseases. Are you to suggest that every single one of these insertions must be functional somehow, when in most cases we've never found a function for any of them? A lot of them are just degenerated viruses, afterall. And they mutate at the neutral rate, demonstrating that they're not under selection.

Well maybe I shouldn't be surprised since you're all scientists. Maybe scientists and engineers are different species . . .

Maybe so. I've never known a scientist to tell an engineer that he knew more about enigneering than the engineer did, despite having made numerous laughably ignorant statements demonstrating that he did not, in fact, know the first thing about engineering.

So how much of the amoeba dubia genome is non-functional junk? You speak as if you know the answer without a doubt. You must have completely sequenced it, figured out what each bit of it does, and kept it a secret.

Now your projecting, Dave. You see, it's your theory which requires not only that the entire A. dubia genome is functional, but that it contains genes that it doesn't need at all and are being preserved by some mysterious process for some future point in time when it evolves into a human being in a remarkable (and never before seen) feat of parallel evolution. Please tell me, where's the evidence for that? I'm quite sure that a large chunk of the A. dubia genome consists of noncoding regions that at most only function as spacers, because it's this way in all eukaryotes. A. dubia in particular has far more DNA than closely related species, indicating that a common means of genomic expansion (polyploidy or retrotransposition) was probably at work. You see, this is the difference between an informed hypothesis based on sound theory and a WAG based on ignorance of basic biology.

I said at the start that the theories were mostly based on junk DNA. Like that's a tough one to come up with. Duh.

Except you were wrong, and it appears that you still adhere to this mistake, demonstrating that you haven't actually read any of that review beyond the first paragraph or two.

Equally obvious is selection pressure to make it smaller. Duh again. I already explained that there's a high energy cost associated with DNA replication which you pooh-poohed out of hand so I guess you're aligning yourself the "it's all just junk" theory.

No, wrong again. My point was that you cannot rule out the theory that there is no selective pressure to remove extra DNA because it does not have high energy costs in most situations. The situations in which extraneous DNA gets removed tend to occur in organisms that are likely to have selective pressure to remove it. It also correlates quite well with cell size, which is of course the basis of nucleoskeletal and nucleotypic theories, which you have managed to pooh pooh out of hand. Actually, you haven't even acknowledged their existence, preferring simply to believe that if there isn't a complete consensus on what the precise cause is, then your own obviously wrong hunch must be correct.

My explanation for c-value is not remotely plausible, eh. Which god of truth died and made you the arbiter of plausibility?

I've already explained why your idea contradicts basic knowledge of molecular biology (which means, I'm wasting time repeating myself). You even manange to contradict your own pan-selectionist reasoning. If everything must be there for a purpose, then it's mighty hard to explain how a gene which will only be useful millions of years from now manages to escape silencing mutations and deletion. Not to mention the fact that we just don't see large numbers of genes anyway; most DNA is noncoding. There are no known organisms harboring massive amounts of genes that they have no use for, genes which just so happen to be present in organisms that are derived. If we did see such a thing, it would be strange indeed.

racingiron · 20 January 2005

DaveScot, I'm wondering about your following statement:

DaveScot wrote: Computers are already evolving millions of times faster than anything biological. I think the more practical track is to take what we've learned from the artifical evolution of computers and apply it to biological evolution in search of answers to some of the more intractible questions.

Are you saying that computers themselves (hardware) are evolving, presumably via the human "design" process? Please forgive me if I've misunderstood you.

Grand Moff Texan · 20 January 2005

Perhaps we can take heart from the apparent fact that DaveScot has graduated from mere superstition to citing (perhaps randomly generated) metaphors? Or is the false analogy fallacy just another tool of "Intelligent" Design?

Damn. Thought we were making progress.

Don T. Know · 23 January 2005

Just because you don't understand the function of any given bit of DNA doesn't make it not required for reproductive success

So, there is no such thing as genetic "junk" since we may not "understand the [reproductive] function of any given bit of DNA."

jackd · 23 January 2005

imagine how much money AT&T saves with a 0.1% improvement in compression - it seems small but multiplied by the untold billions of dollars in their voice switching capacity it's BIG money. But I digress . . .
— DaveScot

A digression, but telling in one sense. I was in AT&T network planning twelve years ago. That 0.1% improvement wasn't going to save AT&T one stinkin' dime. Anyone who knows about circuit-switched networks (e.g. AT&T, the "Baby Bells", and practically every pre-VoIP network in existence) would know that bandwidth per circuit is fixed at 56 or 64kbps. The big voice switches (4ESS, 5ESS, DMS100, etcetera) switch voice channels at DS0. The best compression algorithm in the world wouldn't change that, and only a complete overhaul of the network hardware and software would allow AT&T/Sprint/MCI/whoever to use compression to make the overall network more efficient. For specific applications where bandwidth is expensive and you can increase the total number of channels - satellite links, for example - compression is quite valuable. Cellphone technology might use it a lot (not my area). But it was never going to be an issue for what used to be called the Public Switched Telephone Network.

Wayne Francis · 23 January 2005

Jackd - don't argue with DaveScot....without him we wouldn't have the computers we have today!

programs created from GAs (programs writing programs) don't exist because he says so!

Our 4 seasons are scientific fact and could not be interpreted anyother way because he says!

DaveScot is my hero.

But I digress....thanks for the insight to another area of DaveScot's imaginary world.