I think I had one too many
by MikeGene
HT: Jason
21 Responses to “I think I had one too many”
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The Design Matrix: A Consilience of Clues by Mike Gene 
Your Inner Fish: A Journey into the 3.5-Billion-Year History of the Human Body 
Catalyzing Inquiry at the Interface of Computing and Biology 
System Modeling in Cellular Biology: From Concepts to Nuts and Bolts 
The Plausibility of Life By Marc W. Kirschner and John C. Gerhart 
Agents Under Fire by Angus Menuge 
Life's Solution by Simon Conway Morris 
Information Theory, Evolution and the Origin of Life by Hubert P. Yockey 
The Fifth Miracle by Paul Davies 
Nature, Design, and Science by Del Ratzsch 
Origination of Organismal Form by Muller & Newman 
Biased Embryos and Evolution by Wallace Arthur 
Rare Earth by Peter Ward and Donald Brownlee 
The Privileged Planet by Guillermo Gonzalez and Jay Richards 
The Way of the Cell by Franklin Harold 
The Volitional Brain by Benjamin Libet 
Evolution in Four Dimensions by Eva Jablonka & Marion Lamb 
The Evolution-Creation Struggle by Michael Ruse
September 3rd, 2007 at 1:18 am
LOL!
Comment by Bradford — September 3, 2007 @ 1:18 am
September 3rd, 2007 at 11:25 am
OK, this educated layman has a question for you biology types out there.
I have heard two things said about the human genome that seem to me to be contradictory. I was wondering if anyone could reconcile them.
The first thing is that we have something like 98% genetic similarity to the chimpanzee. I take this to mean that, if I ran some sort of differentiating program on them, with each nucleotide on a separate line, then the number of lines that are in continuous similar blocks with each other would add up to 98% of the length of the genome.
The second thing is that some huge portion of the genome - like 95% or something - is more or less junk. It has no function in the organism. I take this to mean that if we scrambled the information in these segments, the organism would continue functioning just fine (as long as in our scrambling we didn't coincidentally code for some "kill the organism" protien).
These things seem completely at odds to me. If a portion of the genome is junk, than there is no selective pressure to keep this portion the same. In fact, there may be a functional advantage in removing it altogether (the organism can get by with less nucleotides in its cells). Over time, these sections would become completely scrambled. The chimp and the human genome would then look almost nothing alike - maybe 98% of that remaining 5% that actually does something would be similar.
So…anyone want to clear things up for me? What is missing in this picture?
Comment by Wonders For Oyarsa — September 3, 2007 @ 11:25 am
September 3rd, 2007 at 11:41 am
Wonders For Oyarsa making a case against junk DNA assumptions:
Generating actual junk is metabolically wasteful and you are correct in believing there would be a selective advantage to a means of removing it. The sequential order of such regions should become increasingly unrecognizable with time. In fact, if such genomic regions are non-functional then there should be no expectation of uniformity even among individuals of the same species. So why is there an expectation that different species retain such recognizable regions of non-function when natual selection plays no sifting role? Such questions lead me to think current paradigms are based on a combination of lack of knowledge and a viewing lens that skews our understanding of what is actually occurring.
Comment by Bradford — September 3, 2007 @ 11:41 am
September 3rd, 2007 at 12:25 pm
My case only holds if my assumptions of what 98% similarity and 95% junk mean are correct. It's such an obvious conclusion, that I'm inclined to assume I am misinterpreting something. I would like to be educated as to exactly what that something is.
Comment by Wonders For Oyarsa — September 3, 2007 @ 12:25 pm
September 3rd, 2007 at 12:59 pm
I'm not a biologist, but five minutes with Google and wikipedia is enough to learn that current thinking is that "junk DNA" is probably a misnomer, and what we really have is DNA whose function is not yet known.
Another thing to keep in mind is that the human genome is about 3 billion base pairs long, so a 2% difference is 60 million mutations. Sounds less trivial that way, doesn't it?
Comment by mtraven — September 3, 2007 @ 12:59 pm
September 3rd, 2007 at 6:16 pm
What is being compared, Wonders, and how is it being compared?
Comment by Rock — September 3, 2007 @ 6:16 pm
September 3rd, 2007 at 9:12 pm
Rock,
If someone would tell me that, I would certainly appreciate it. One interesting thing to keep in mind is that, if memory serves, people were using the 98% statistic before the human genome was sequenced.
Comment by Wonders For Oyarsa — September 3, 2007 @ 9:12 pm
September 3rd, 2007 at 9:25 pm
Wonders-
The genome consists of the entire DNA present in the nucleus of the fertilized embryo, which is then duplicated in every cell in the body. A draft sequence of the chimpanzee genome is now available, providing opportunities to better understand genetic contributions to human evolution, development, and disease. Sequence differences from the human genome were confirmed to be 1% in areas that can be precisely aligned, representing 35 million single base-pair differences. Some 45 million nucleotides of insertions and deletions unique to each lineage were also discovered, making the actual difference between the two genomes 4%.We discuss the opportunities and challenges that arise from this information and the need for comparison with additional species, as well as population genetic studies. Finally, we present a few examples of interesting findings resulting from genome-wide analyses, candidate gene studies, and combined approaches, emphasizing the pros and cons of each approach.
Emphasis added by me.
Comment by Bradford — September 3, 2007 @ 9:25 pm
September 3rd, 2007 at 10:13 pm
Ahh - so the actual number is 96%. But it does look more or less like what I was talking about. In which case it is almost certain that the entire genome is pretty important stuff, even if it isn't doing protein coding.
Comment by Wonders For Oyarsa — September 3, 2007 @ 10:13 pm
September 3rd, 2007 at 10:13 pm
Thanks Bradford - that answers my question.
Comment by Wonders For Oyarsa — September 3, 2007 @ 10:13 pm
September 3rd, 2007 at 11:50 pm
For anyone who missed it:
My retreat from the public view"¦
I'll miss haning out with you all.
Thanks for all the good times.
Sal
Comment by Salvador T. Cordova — September 3, 2007 @ 11:50 pm
September 4th, 2007 at 12:11 am
Salvador, you will be missed. Your input is valued.
Comment by Bradford — September 4, 2007 @ 12:11 am
September 4th, 2007 at 11:01 am
Hey Mike, now that I've been given more information, would it be worth my while to spruce my initial comment up and flesh it out to be used as a guest post?
Comment by Wonders For Oyarsa — September 4, 2007 @ 11:01 am
September 4th, 2007 at 11:10 am
Wonders For Oyarsa, I'm not speaking for Mike but why not give it a try?
Comment by Bradford — September 4, 2007 @ 11:10 am
September 4th, 2007 at 7:40 pm
Hi WFO,
Sure. In fact, I'm happy to consider submissions from any long time user here (remember folks, the opportunity exists only for the remainder of this year). But I would caution that there is a hole in your argument. Since chimps and humans split only about 5 million years ago, you have to factor whether or not there has been enough time for mutation to "completely scramble" non-coding sequence.
Comment by MikeGene — September 4, 2007 @ 7:40 pm
September 4th, 2007 at 7:59 pm
Nah, Mike - I think your intuition is way off here. It is commonly said that most mutations are actually harmful. But in the case of junk, most mutations do nothing - and as such natural selection wouldn't care one way or the other about them. The amount of scrambling you'd have to statistically get a good mutation would be tremendous.
But don't take my word for it. I'll code up a little flash simulation involving killer mutating asexual bunnies to prove the point. Stay tuned…
Comment by Wonders For Oyarsa — September 4, 2007 @ 7:59 pm
September 4th, 2007 at 8:04 pm
Whoa! I'm drooling. I'm sensing Post of the Month here.
Comment by MikeGene — September 4, 2007 @ 8:04 pm
September 7th, 2007 at 2:31 pm
As a Computer Scientist, I never was terribly impressed by the notion of "junk DNA". The idea that 90% of our DNA has no function is counter-intuitive at best. The human genome already seems to be surprisingly small to specify all the information required to describe how to build a human being from a single cell (implying to me some pretty good compression), and further reducing this to the information content of Microsoft Office is not what I would expect. But then again, life isn't always intuitive. Stranger truths have been found in nature, so I suppose we need to keep an open mind.
Then I remembered that we have around 96% genetic similarity to the chimpanzee - meaning large chunks of our genome can be matched up with chunks of the chimp genome almost exactly. These things seem completely at odds to me. If a portion of the genome is junk, than there should be no selective pressure to keep this portion the same. In fact, there may be a functional advantage in removing it altogether (the organism can get by with less nucleotides in its cells). Over 5 million years, it certainly feels like these junk sections would become completely scrambled, rather than maintaining almost total similarity.
So, what better way to demonstrate this than with the clear irrefutable scientific proof of a toxic asexual bunny mutation simulator?
[ insert bunny mutator here ]
Rules:
Toxic asexual bunnies are, well, toxic. As such, they are dangerous to everyone, including each other. A mere touch by one toxic bunny to another may be enough to kill it, though some have been known to evolve greater toxin tolerances (which in turn make them more deadly to other toxic bunnies).
- Each bunny has a DNA string of 30 English characters.
- The toxin defense gene is located in the first three characters, which must spell an English word.
- Furthermore, the organism has evolved such that only an English word starting with "BU" is sufficient to defend it under these conditions (we are simulating only a small evolutionary change).
- Each sample starts with the same bunny with the first three letters as "BUN". The rest of its genome is junk, designated by dashes for the sake of easy reading.
- As the bunnies reproduce, random mutations take place. Most of these mutations will do nothing since it occurs in the junk, but some will occur in the first three letters.
- If the mutation occurs in the first two letters, it is a harmful mutation.
- If it occurs in the third letter, there is a 1/4 chance of a new word generated, indicating a functional advantage.
- Once new bunny species dominate both groups, the new genomes are compared.
Results:
As I expected, getting a positive change in a single character to a new spices garbles the junk DNA to near oblivion. I'm getting a statistical average of about 35% similarity - a far cry from 96%, and not to far from the 9% or so that would indicate total scrambling.
Qualifiers
Obviously the mutations are sped up in my simulation, and I am not including many of the different types of mutations that actually occur (reversals, additions, deletions, splitting, moving, etc). The sample sizes of human and chimp populations are much larger than the ten or so that I show. But I think this easily offset by the sheer size of the genome, as well as the improbability of getting a truly helpful mutation that would provide a serious functional advantage.
I think the simulation sufficient to illustrate the principle - that getting a good mutation in a small area requires a large number of neutral mutations across the board (in the case of junk DNA).
Conclusion:
Folks, the bunnies don't lie. We might not know what this stuff does, but it sure ain't junk.
Wonders for Oyarsa is a programmer somewhere in the United States. When he's not working full-time, pursuing his M.S. in Computer Science part-time, and raising two kids, he likes to investigate the notion that intelligent design was involved in the writing of the Bible on his blog.
Comment by Wonders For Oyarsa — September 7, 2007 @ 2:31 pm
September 7th, 2007 at 2:33 pm
Hey Mike - is there an email address I can send the bunny simulator SWF to? I'd like it to run inline with the post - it needs to be 400 Wide by 500 Tall.
Comment by Wonders For Oyarsa — September 7, 2007 @ 2:33 pm
September 7th, 2007 at 2:44 pm
You can send an address to me if you don't want to post on the web: wondersforoyarsa AT yahoo DOT com.
Comment by Wonders For Oyarsa — September 7, 2007 @ 2:44 pm
September 7th, 2007 at 9:55 pm
WFO,
Check your email
Comment by MikeGene — September 7, 2007 @ 9:55 pm