No Junk DNA vs. Rarity of Function

Design

(Bill Cole) #41

What are those odds? Very low. The human genome is composed of over three billion nucleotides. Yet only a hundred million nucleotides seem to be critical, coding for proteins or necessary control features.

The other was found on google search. This I found in the book. I think his position is pretty clear.

Behe, Michael J… The Edge of Evolution: The Search for the Limits of Darwinism (Kindle Locations 1753-1754). Free Press. Kindle Edition.


#42

Just to be clear, I am not saying that ID must take the position that there is no junk DNA. The point I am trying to make is that if an ID supporter says that there is no junk DNA then it leads to the conclusion that most random DNA sequences have function. As I said earlier, you can choose no junk DNA or rarity of function, but you can’t choose both.


(Bill Cole) #43

Why cant you have no junk and some of the genome is very sequence specific and some is not. Introns may be important spacers during embryo development but sequence may be less critical then exons.


#44

I would guesstimate that introns make up maybe 5% of the genome, or somewhere around there. That leaves a lot of the genome that isn’t introns and is still claimed to have function. ID supporters have cited pervasive transcription of non-coding DNA as evidence for function, so I would have to think that they are pushing for function in those RNA molecules outside of spacing between exons, and it would seem to require some sort of sequence specific activity.


(Bill Cole) #45


#46

I thought we had agreed that it is not an either/or choice. You can have rarity of function depending on how you choose to define function. All DNA can have function depending on how you define function.

The function of DNA is to store biological information and allow for the evolution of populations of organisms. All DNA serves that function regardless of whether it is “junk” or not.


#47

If you define function so that nearly any DNA sequence has function then you can’t claim that function is rare. If you are going to argue for a lack of junk DNA in the human genome then you have to use the most permissive definition for function, hence function isn’t rare.


#48

I believe that you can. The reason that I think you can hangs on the fact that what is meant by “function” can change depending on how it is defined, context, etc. Surely you are familiar with the concept of equivocation. The same word can have more than one meaning. I’m not going to keep repeating myself so this may be my last comment on that point. Regards


#49

If you define function in such a way that function is found very rarely in DNA sequences what percentage of the human genome would have function according to this definition?


#50

It would depend on the definition. Defining function as function that is rarely found is to define the term by reference to the term. That’s normally not allowed.

Do you think it’s worth debating whether we could define a function that would be “rare” in “DNA sequence space”? How about a hydroelectric dam that puts out the same or greater amount of power as the Three Gorges Dam in China? Rare in DNA sequence space? Probably.


(S. Joshua Swamidass) #51

@Mung, I’d prefer to see you debate with someone from your own camp (ID) the extent of “function” in DNA. That might actually get us somewhere. I see no real value in you and @T_aquaticus hashing it out. Are you up for clarifying this point with some ID advocates?


#52

Scientists certainly debate this question, and they find it worthwhile. ENCODE defined function as participating in a biochemical reaction, and by extension this is the definition used by many ID supporters. When we use this definition, about 80% of the human genome has function.

If we define function by “it could lose its function through mutations”, which is the definition preferred by most biologists, then about 10% of the human genome has function.

When using the ENCODE definition, almost any DNA sequence will have function. Random sequence will naturally have sequences that weakly bind transcription factors that results in low level transcription, as one example. This is the definition one has to use in order to claim that a large percentage of the human genome has function.

If you use the definition of function based on sequence conservation then random DNA will rarely have function. You will also find that only 10% of the human genome has function under this definition.

The more restrictive your definition is for function the more junk DNA you find in the human genome.


#53

I’m somewhat infamous for disagreeing with other IDists. I’ve disagreed with Bill Cole both here and elsewhere as just one example. If you watch closely, you will see that I don’t play favorites. Take for example my question to Ann when I asked about the absence of any case FOR common descent in the Theistic Evolution book. To her credit see took the question seriously.

What is your opinion about working with small sample sizes?

Of course. Do you think you can get Jonathan Wells to come here?


(Ann Gauger) #54

@Swamidass, parse the sentence.

  1. unless functional sequences are easy to find (very common), and/or are clustered together (easily reachable from one functional island to another)”: I think you agree with the statement. I am laying out the conditions where it might be possible to convert function.
    2." explaining current protein diversity without design is impossible." Unless the above conditions are met, namely that functional sequences are easy to find or clustered together, we won’t be able to find functional sequences.

Turn the sentence around.
Explaining current protein diversity without design is impossible, unless functional sequences are easy to find (very common), and/or are clustered together (easily reachable from one functional island to another).

Maybe take out intelligent design if you deny the possibility of design at all:
Explaining current protein diversity is impossible, unless functional sequences are easy to find (very common), and/or are clustered together (easily reachable from one functional island to another).

I am talking about finding functional sequences by a random mutational walk through non-functional sequence space, which means that functional sequences are common to start with, or are close by in sequence space and easy to find.

Do you agree with that? If not, what do you believe?


(Ann Gauger) #55

@T_aquaticus
I like what you have written and it would be my position with a little modification.

  1. Functional sequence in the sense of ENCODE is sequence with any biochemical activity at all. Transcription, methylation, a site for DNA binding etc Even ENCODE workers admit they don’t know how much of that “function” will be meaningful.
    2.In the ENCODE sense, most genomic sequence is functional, thus functional sequence is common (20-80% was the original range offered). Just remember what function means here.
  2. When we say functional sequence is rare in sequence space, we mean a different sort of function. We mean the ability to carry out an enzymatic reaction. It is our claim that proteins made from random sequence will rarely have any sort of enzymatic activity. Mung was right when he said in one case we were talking about DNA function, and in the other, protein.
  3. That is why experimental tests are important. Can random DNA sequence produce functional proteins with enzymatic activity.
    Our prediction is that such experiments will fail, because of the inability to test enough sequence to detect such a small signal. YET if you look at the actual number of orphans, that suggests design.

#56

I would assume that you also consider function to include molecules that bind to other molecules without carrying out an enzymatic function, such as microRNA or antibodies. I think we would also agree that promoter regions and other DNA features are functional as well. IOW, function is defined by sequence. Change the sequence and you change the function, or possibly lose it.

With that said, I completely agree that this is the type of function you have been consistently talking about, and it is one that most biologists are very familiar with. Using this definition, only a small percentage of the human genome has function. There are plenty of other threads where we can go back and forth about the availability of function in DNA sequence, but the main point I wanted to get across is that there is an interplay between how one defines function and how one measures junk DNA. At least for the human genome and most other eukaryotic genomes, if you define function in a meaningful way you would have to conclude that there is a lot of junk DNA.


(Dan Eastwood) #57

Ann, Thank you for stating your position so clearly for us. Without a common basis of understanding people end up talking past one another. You have given me something I can think about as a serious idea, and I will consider it carefully. :slight_smile:


(John Mercer) #58

Doesn’t the body of catalytic antibody literature clearly answer your question in the affirmative?

So I would presume that you would see such experiments as important to perform yourself. What experiments are you doing, and how would they be more illuminating than the catalytic antibody experiments that have been done?


(Ann Gauger) #59

@Mercer
That’s an interesting example. Using the power of the immune system to search for a protein that binds to a hapten that resembles the transition state of the reaction desired is pretty ingenious. I’d have to read some papers to see how the work was done. But that’s a designed system, making use of an elegant system to target a desired reaction and refine its specificity over time.

As for the last, I would be performing these experiments myself, except I have developed an essential tremor, that gives me shaky hands. I can’t pipet or maintain sterile culture. I haven’t been in the lab for several years.


(S. Joshua Swamidass) #60

@agauger, that is not accurate. It is a system designed to mimic an undesigned process. This is necessary because it is exceedingly difficult to to select for enzyme activity in an in vitro system, for purely technical reasons. The “design” you are seeing is merely a trick to enable the in vitro system mimic the in vivo reality.

I am resistant to this objection too, because it is contradictory with the demands to reproduce evolutionary changes in vitro in the laboratory. All in vitro in lab experiments involve human intelligence. If this is a valid objection, than it is disengenuous, or at least self-contradictory, to demand in vitro evidence of the evolution of new enzymes.