Understanding through Discussion


Welcome! You are not logged in. [ Login ]
EvC Forum active members: 89 (8890 total)
Current session began: 
Page Loaded: 02-15-2019 4:49 PM
198 online now:
AZPaul3, caffeine, JonF, Meddle, PaulK, Phat (AdminPhat), Theodoric (7 members, 191 visitors)
Chatting now:  Chat room empty
Newest Member: WookieeB
Post Volume:
Total: 847,542 Year: 2,579/19,786 Month: 661/1,918 Week: 249/266 Day: 21/92 Hour: 2/0


Thread  Details

Email This Thread
Newer Topic | Older Topic
  
1
234567Next
Author Topic:   How well do we understand DNA?
TheLiteralist
Inactive Member


Message 1 of 98 (177444)
01-16-2005 1:12 AM


Mutations, On-purpose Randomness, & Junk DNA
Some other thread discussions have made wonder some things...


  1. How well do we understand DNA in general? I'm not referring to the human genome specifically. Any genome...maybe something simple like a bacterial genome. Are we able to say, "Okay, if we connect these 50,000 base pairs in this sequence we will get these results?"

  2. Are we certain that all changes in DNA sequences are a result of random mutations--i.e., copying errors? This question is inspired by experiments wherein supposedly one bacterium develops a colony with many variants. How do we know that there is not some method within the genome that is supposed to generate some level of variation--i.e., it's not random mutations but rather variation achieved through randomness generated purposefully by the code? A limited experience in programming has taught me that in many programs it is often useful to have a random generator module. For instance, if I wished to write a code for the game Solitaire, I would, somewhere, have a random generator to come up with the card order. However, the randomness would be purposefully limited in what it could affect. It couldn't, for instance, ever cause the game to become Poker. There would be certain modules that I would not want to ever want to be affected by the random generator, and should something happen (like a power spike) to "randomly mutate" those modules, the program either would not run at all or, at least, would not run optimally.

    Therefore, IF the genetic code is by intelligent design, how would we differentiate between random mutations and purposeful, limited randomness--and has this already been done somehow? (I'm trying to make it clear, but I don't know if I'm succeeding.)

    This idea is specifically pointed at the idea of limits within "kinds" of creatures.

  3. What is JUNK DNA? Another post referred to it as DNA that doesn't regulate or get transcribed. (I have heard, I think, that it is a build up of left overs from ancestors.) Is it possible that this junk DNA DOES perform some function, and we simply either have not observed it as yet or have observed it and didn't know what we were seeing? Could it be acting as a data base for potential features (just an outright guess based on no facts at all)? What have we seen "junk" DNA do or not do that has caused us to dub it as "junk?"

I would particularly like to hear from those whose fields are related to DNA or in some manner. I may not agree with you at all, but I would very much like to know your opinions on the matter as well as the reasons you hold such opinions.

These are areas of genetics I've done no prior study in; so I will likely not be able to debate the topic much (of course, if I feel like I can, I will try).

Also, my background in biology is high school level; so please, if possible, keep things to the layman's level.

Thank you very much.
--TheLiteralist

{edited to add italics to a word--I'm sure it made the OP MUCH clearer!}

{edited again to strike through a couple of repeated phrases (copying errors?...heh)}

{edited...ooh ooh...just noticed the optional Sub-Title...gotta have it}

This message has been edited by TheLiteralist, 01-16-2005 01:13 AM

This message has been edited by TheLiteralist, 01-16-2005 04:04 AM

This message has been edited by TheLiteralist, 01-16-2005 04:06 AM


Replies to this message:
 Message 3 by RAZD, posted 01-16-2005 1:48 AM TheLiteralist has responded
 Message 12 by crashfrog, posted 01-16-2005 1:07 PM TheLiteralist has not yet responded

  
AdminNosy
Administrator
Posts: 4754
From: Vancouver, BC, Canada
Joined: 11-11-2003


Message 2 of 98 (177447)
01-16-2005 1:17 AM


Thread moved here from the Proposed New Topics forum.
  
RAZD
Member
Posts: 19729
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 5.1


Message 3 of 98 (177454)
01-16-2005 1:48 AM
Reply to: Message 1 by TheLiteralist
01-16-2005 1:12 AM


1. Not well but getting better all the time. Ask me again in 2 years.

2. We know that some genetic sequences are more susceptible to mutation than others. My personal opinion is that the rate of mutation has evolved to match the need for it by regulating the level of susceptibility. An organism that mutated too much would have trouble finding mates, while an organism that mutated to little wouldn’t have enough variation “in the bank” to survive natural selection events. It is also logical that if this is the case, that a stressed population can turn up the rate of mutation by turning down the regulating mechanism with stress signals. Again, certain gene sequences could be more affected than others so you would have your “random module” in the sequences most likely to result in viable variations and less in the ones that would result is non-viable variations.

3. Personally I don’t think any DNA is junk, just that the purpose is not known or understood enough. Consider that it takes a considerable expenditure of energy to produce these sequences, and that if they did not serve a purpose that they would be eligible for being weeded out by selection, especially in stressed populations (starving, insufficient nutrients, etc), and that is not happening.

That’s my take on this. :)


we are limited in our ability to understand
by our ability to understand

RebelAAmerican.Zen[Deist
{{{Buddha walks off laughing with joy}}}


This message is a reply to:
 Message 1 by TheLiteralist, posted 01-16-2005 1:12 AM TheLiteralist has responded

Replies to this message:
 Message 4 by TheLiteralist, posted 01-16-2005 3:54 AM RAZD has responded
 Message 6 by Sylas, posted 01-16-2005 4:27 AM RAZD has responded

  
TheLiteralist
Inactive Member


Message 4 of 98 (177470)
01-16-2005 3:54 AM
Reply to: Message 3 by RAZD
01-16-2005 1:48 AM


Are Mutations Assumed or Proven, Though?
Hi RAZD,

Thanks very much for your reply.

2. We know that some genetic sequences are more susceptible to mutation than others. My personal opinion is that the rate of mutation has evolved to match the need for it by regulating the level of susceptibility. An organism that mutated too much would have trouble finding mates, while an organism that mutated to little wouldn’t have enough variation “in the bank” to survive natural selection events. It is also logical that if this is the case, that a stressed population can turn up the rate of mutation by turning down the regulating mechanism with stress signals. Again, certain gene sequences could be more affected than others so you would have your “random module” in the sequences most likely to result in viable variations and less in the ones that would result is non-viable variations.

Of course, I wouldn't expect you to share my views. However, I wonder if you could work, temporarily, from the Intelligent Design premise. I contemplate that somewhere (or many somewheres) the sequences FORCE variation on purpose and in a limited, controlled manner so as to make living organisms both interesting and resilient. And, even, from this view, the Designer would have considered the various stressors of the environment, which He also designed, and so could have made the sequences somehow able to react to triggering stresses.

It just seems like an at least equally valied way of interpretting the whole DNA thing. My knowledge of the subject is so limited, though.

But my question is really: Are mutations assumed or proved? And, if proved, how exactly? Because, I think it would require that the entire code be fully understood in order to prove this assertion. So, if the code is not fully understood, then I don't see how it can be asserted (though it can be assumed) that the DNA variations are resulting from random mutations. I keep hearing "copying ERRORS," but how do we know that those are errors? What if the code is doing exactly what it is supposed to be doing--i.e., creating a certain amount of variation within certain limits?

(I wouldn't necessarily expect you to be able to answer RAZD, though perhaps you can--I'm just really curious about this and kinda thinking out loud.)

Personally I don’t think any DNA is junk, just that the purpose is not known or understood enough. Consider that it takes a considerable expenditure of energy to produce these sequences, and that if they did not serve a purpose that they would be eligible for being weeded out by selection, especially in stressed populations (starving, insufficient nutrients, etc), and that is not happening.

Given the astoundingly detailed ways that nature does things (from either POV), I would consider such a view the logical choice if working from the evolution paradigm. If working, as I am, from the Creation paradigm, then there should be almost, or utterly, no "junk" DNA (some renegade sequences possibly having developed since the Flood due to existence in the wrecked, far-less-than-optimal, no-longer-Edenic environment).

Thanks,
--TL


This message is a reply to:
 Message 3 by RAZD, posted 01-16-2005 1:48 AM RAZD has responded

Replies to this message:
 Message 10 by RAZD, posted 01-16-2005 11:56 AM TheLiteralist has not yet responded

  
socalsp3
Inactive Member


Message 5 of 98 (177472)
01-16-2005 4:21 AM


Hi there,
I've done programming and I've had some biology in college hopefully my response is helpful.

1. DNA is the genetic material. It's the only thing that gets transferred from generation to generation. So yes if you connect the right nucleotides (base pairs) that encodes an organism you want together and stick it into an empty nucleus in an egg of another. You would get the one you intended.

2. This is the question most people have about evolution and most difficult for them to grasp. How can something so complex arise out of random mutation and selection? Well, 4 billion years worth is a start. The earliest organisms we've found are microbes and they are 4 billion years old. Back to the question....How evolution works is that organisms adapt to their present environment. They can't anticipate what they need 1 million years later and start evolving to that form. In your example of a computer program, you wrote it in perfect form to be able to work in its present environment. Now suppose, the environment changes. Say... your compiler gets buggy. It no longer translates some command to its appropriate assembly code. But lets say you compile your program with another program called "natsel.exe" that can detect where your program failed. "natsel" will randomly replace the bug with alternate commands until it finds one that works with the compiler. Most the replacements will not work, but eventually one will work.

What i'm try to get at is that you have to look at the organism within context of its environment though its history. What its form is today is the form it needs to survive in today's environment. Organisms are always changing(because they have to cope with the changing environment) so you can't compare them to a car or a finished product. So you cannot say what if I took away this part here how can it survive. Organism don't change that fast as you can see.

It's getting too late maybe i'll finish tomorrow.


  
Sylas
Member (Idle past 3302 days)
Posts: 766
From: Newcastle, Australia
Joined: 11-17-2002


Message 6 of 98 (177473)
01-16-2005 4:27 AM
Reply to: Message 3 by RAZD
01-16-2005 1:48 AM


RAZD writes:

3. Personally I don’t think any DNA is junk, just that the purpose is not known or understood enough. Consider that it takes a considerable expenditure of energy to produce these sequences, and that if they did not serve a purpose that they would be eligible for being weeded out by selection, especially in stressed populations (starving, insufficient nutrients, etc), and that is not happening.

There is some indication that sheer bulk of DNA carries some selective benefit. Bases added to DNA simply for the sake of bulk are legitimately called junk.

Sample reference of many: Cavalier-Smith, T. Skeletal DNA and the evolution of genome size. Annu. Rev. Biophys. Bioeng. 11:273-302 (1982). Ref pinched from bibliography of Evolutionary Principles of Genomic Compression by David C. Krakauer.

We also know that different parts of the genome have different selective pressures. Some sequences are highly conserved; others are not. In fact, this is one way of identifying sequences that have some importance, even if we don't know their role! One mystery is that some high conserved sequences were deleted from mice, with no apparent effect. This remains a mystery.

Ref: Are Ultra-conserved Elements Indispensable? by Dr Mae-Wan Ho (ISIS press release, 16/09/04).

But by comparison there are other parts of the genome where mutations accumulate at pretty much the same rate as they arise, indicating no selective pressures at work. This is indirect evidence for junk, I suggest.

Cheers -- Sylas


This message is a reply to:
 Message 3 by RAZD, posted 01-16-2005 1:48 AM RAZD has responded

Replies to this message:
 Message 8 by RAZD, posted 01-16-2005 10:17 AM Sylas has not yet responded
 Message 21 by TheLiteralist, posted 01-23-2005 12:42 AM Sylas has not yet responded

  
Nic Tamzek
Inactive Member


Message 7 of 98 (177476)
01-16-2005 5:26 AM


The amount of DNA per cell is highly correlated with the cell volume of the species.

This fact favors either a "skeletal DNA" explanation (sheer bulk of DNA has some function, but not any "complex" sequence-specific function), or a "pure junk" explanation (for large cells, DNA replication costs are trivial compared to other biochemical processes).

The fact that the amount of DNA can vary widely even between two closely related species, and that large chunks of DNA can be deleted in some organisms without apparent ill-effect, strongly indicates that some DNA really is junk.

See http://www.evowiki.org/index.php/Junk_DNA for graphics and references.


  
RAZD
Member
Posts: 19729
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 5.1


Message 8 of 98 (177519)
01-16-2005 10:17 AM
Reply to: Message 6 by Sylas
01-16-2005 4:27 AM


Interesting Sylas, thanks.

I don't equate expendable with junk, but rather with redundant, and I think it is entirely valid to have redundant systems that rarely get used. Those "highly conserved" sequences would certainly qualify for preserved redundancy, and this may be a secondary function of the extra sequences - to keep the "conserved" sequences operational. An offshore sailing vessel with no redundancy in it's life support systems is asking for trouble when any one of them goes down. Redundant genetic material can ensure that a match-up of working genetic sequences during the reproductive process can occur (or rather before, with the repair mechanisms, and multiple copies just means that you have a higher correlation of what is a "good" sequence compared to what is a "damaged" sequence).

But by comparison there are other parts of the genome where mutations accumulate at pretty much the same rate as they arise, indicating no selective pressures at work. This is indirect evidence for junk, I suggest.

Or evolution has shown that variation within those sequences is not critical to {structure\life\reproduction} while still being necessary for some function within the system as a whole. This falls into the category I discussed (#2) where a species develops viable variations on a working theme ... like hair color as a raw example ... that ensure enough variations are "in the bank" to provide working answers for {survival\sexual} selection tests, while the ones that are more critical to basic viability {heart function, lung function, nerve function} are more strictly conserved.

For there to be "junk" sequences in my mind there would have to be whole sequences that are regularly excluded from the reproductive process, chunks dropped regularly and randomly throughout the population, and I don't see that happening.


we are limited in our ability to understand
by our ability to understand

RebelAAmerican.Zen[Deist
{{{Buddha walks off laughing with joy}}}


This message is a reply to:
 Message 6 by Sylas, posted 01-16-2005 4:27 AM Sylas has not yet responded

Replies to this message:
 Message 9 by NosyNed, posted 01-16-2005 10:50 AM RAZD has responded

  
NosyNed
Member
Posts: 8829
From: Canada
Joined: 04-04-2003
Member Rating: 4.5


Message 9 of 98 (177524)
01-16-2005 10:50 AM
Reply to: Message 8 by RAZD
01-16-2005 10:17 AM


Tidying up
For there to be "junk" sequences in my mind there would have to be whole sequences that are regularly excluded from the reproductive process, chunks dropped regularly and randomly throughout the population, and I don't see that happening.

I disagree. If the only processes acting to change DNA are the reproduction process itself, the error correction processes and mutations (of all sorts) then there is nothing to "drop" DNA but those mutations. If random most of these drop "good" as well as "junk". If it is true that the cost of carrying extra DNA is small then there will be no selection acting to get the real junk weeded out.

Also remember that the original designation of junk was based on the fact that it does not code for proteins.

Also we see that what are obviously broken genes are carried along for a pretty significant time. It is unlikely that these are both broken genes and of some other value (unless pure bulk is of value).

I think it is true that bacteria (where there may well be a 'carrying cost' since they are smaller) do not carry as much junk.

This message has been edited by NosyNed, 01-16-2005 10:51 AM


This message is a reply to:
 Message 8 by RAZD, posted 01-16-2005 10:17 AM RAZD has responded

Replies to this message:
 Message 11 by RAZD, posted 01-16-2005 12:22 PM NosyNed has not yet responded
 Message 22 by TheLiteralist, posted 01-23-2005 1:02 AM NosyNed has responded
 Message 29 by Lizard Breath, posted 01-23-2005 7:52 AM NosyNed has not yet responded

  
RAZD
Member
Posts: 19729
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 5.1


Message 10 of 98 (177547)
01-16-2005 11:56 AM
Reply to: Message 4 by TheLiteralist
01-16-2005 3:54 AM


Re: Are Mutations Assumed or Proven, Though?
TheLiteralist writes:

But my question is really: Are mutations assumed or proved? And, if proved, how exactly?

Proved to exist and proved to cause changes. The fruit fly experiments did this many years ago, recent genetic studies have shown exactly where the DNA was changed and what the change was.

Of course, I wouldn't expect you to share my views. However, I wonder if you could work, temporarily, from the Intelligent Design premise. I contemplate that somewhere (or many somewheres) the sequences FORCE variation on purpose and in a limited, controlled manner so as to make living organisms both interesting and resilient. And, even, from this view, the Designer would have considered the various stressors of the environment, which He also designed, and so could have made the sequences somehow able to react to triggering stresses.

There are a several elements here.

(1) A {somewhere\manywhere} generator of variation within the code structure itself.

(2) The question of {intelligent\random} design influence.

(3) The level of involvement of a designer if one is involved

(4) A universe "primed" to generate variation.

Working backwards through this list:

(4): Certainly the ultimate "Intelligent Design" scenario is the {put the whole thing in motion with a maximum degree of variation in all aspects of the universe with the universe "primed" to develop an evolving life where-ever conditions are favorable} and then proceed from there with several alternatives of involvement in "tweaking" the design. As I have said before on other threads, ID ultimately, and properly pursued (click), has no problems with evolution working exactly as science finds it to work. I would be happy to discuss that aspect on the thread linked rather than pursue it here and dilute this discussion.

(3): Clearly there is no active, highly involved, hands on designer, or there would be evidence of {his\her\their\its} many perturbations on the natural world. This means that active involvement must be very low and that means that any system involved had to be “pre-wired” to cover the situations to be encountered. Ultimately this becomes indistinguishable from natural systems ... as in:

(2): The problem of the design question is to be able to differentiate {natural\random\unguided} design from {intelligent\intended} design when both can generate very complex and similar solutions. We see software programs now that are set up to “evolve” solutions to the {programming need} without the programmers needing to know how to solve the {programming need} or even how the code works once evolved.

One example of such a {natural\random\unguided} design is the observed natural development of an “Irreducibly Complex” system. See "A True Acid Test" (click) for an article on this (wish I had a reference that wasn’t as pyric as this though). The key point in it is:

Achieving Irreducible Complexity
The three parts of the evolved system are:
(1) A lactose-sensitive ebg repressor protein that controls expression of the galactosidase enzyme
(2) The ebg galactosidase enzyme
(3) The enzyme reaction that induces the lac permease

Unless all three are in place, the system does not function, which is, of course, the key element of an irreducibly complex system.

Thus we have a natural development of what was touted as a clear sign of {intelligent\intended} design if not the hallmark sign. This single such result invalidates the concept of “IC” being a sign of ID (and it is time for the ID proponents to reject IC and develop another testable hypothesis if they want to be considered scientific).

This {natural\random\unguided} design is sometimes referred to as “apparent” design – natural processes that results in an appearance of design even though none was involved (or where the ‘design’ selection is natural). Evolution is full of examples of apparent design, from the eye to the hemoglobin molecule to the whole DNA structure.

{{An interesting sub-example of this process of apparent design is the “Darwin Poetry” experiment
http://www.codeasart.com/poetry/darwin.html
you lie beautiful
beating beyond love
imagine humming forest the soothe disaster ah
leaves hear minutes in what eyes shall go divine

randomly generated lines, selected artificially by random people}}.

I also have referred to apparent design as the “kaleidoscope” syndrome: look in one end of the kaleidoscope and you see a wonderful pattern; look in the other end and you see a random jumble of colored bits and beads. The appearance of pattern is caused by the viewpoint, and the random jumble is the reality.

(1): A {somewhere\manywhere} generator of variation only needs to be a certain level of susceptibility to mutation from outside triggers, UV radiation, chemical exposure, etcetera. In other words, it can use some “stress triggers” as mutation agents in addition to low level constant mutation pressures. This too would account for changes in the rates of mutation when stressed. (Certainly when people are “stressed” they make more mistakes. :laugh:)



My personal (deist) belief is that {supernatural} became the universe intentionally primed for maximum diversity and the evolution of life and intelligence in as many ways as possible with one caveat: “surprise me” ...

Enjoy.


we are limited in our ability to understand
by our ability to understand

RebelAAmerican.Zen[Deist
{{{Buddha walks off laughing with joy}}}


This message is a reply to:
 Message 4 by TheLiteralist, posted 01-16-2005 3:54 AM TheLiteralist has not yet responded

  
RAZD
Member
Posts: 19729
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 5.1


Message 11 of 98 (177556)
01-16-2005 12:22 PM
Reply to: Message 9 by NosyNed
01-16-2005 10:50 AM


Re: Tidying up
ned writes:

I disagree. If the only processes acting to change DNA are the reproduction process itself, the error correction processes and mutations (of all sorts) then there is nothing to "drop" DNA but those mutations.

At least one of those processes, transcription errors during DNA duplication, is capable of dropping sequences, and that is all that is necessary for a stressed population with insuffient nutrients and energy levels to have an advantage in dropping the extra expenditures of protein and energy in the replication of unnecessary sequences.

This to me indicates that there should be random "holes" in the genome sequences of different individuals within a total population (or even between cells within an individual). They don't have to be in any high proportion, but they should show up in a regular and persistent and randomly distributed pattern within the total {individual\cell} populations.

I also do not see any special benefit to single cell species in this regard, as they don't have any more wastefull an expenditure of resources and energy as every single cell in a multi-cellular species. They are rather more likely to require all their sequences than each cell in a multicell species.

This is my opinion on the matter, and we can agree to disagree until more information is available.


we are limited in our ability to understand
by our ability to understand

RebelAAmerican.Zen[Deist
{{{Buddha walks off laughing with joy}}}


This message is a reply to:
 Message 9 by NosyNed, posted 01-16-2005 10:50 AM NosyNed has not yet responded

  
crashfrog
Inactive Member


Message 12 of 98 (177563)
01-16-2005 1:07 PM
Reply to: Message 1 by TheLiteralist
01-16-2005 1:12 AM


I would particularly like to hear from those whose fields are related to DNA

I'm just an amateur, kind of an "armchair biologist", but my wife is a guraduate student working on developing a genetic basis for the classification into species for different varieties of a common agricultural pest. So hopefully you won't consider my input enitrely without merit.

Are we able to say, "Okay, if we connect these 50,000 base pairs in this sequence we will get these results?"

We do have an ability to determine, from a given sequence of nucleotides, what amino acid residues will be connected as a result. That's a pretty simple code. But protein function is a matter of shape, which results from the complicated folding interactions of those residues. While we're working hard on it*, we don't as yet have the ability to predict shape from sequence except for the simplest sequences.

The major surprise of the last few years was how simple our DNA really is, less than 25k genes. We had predicted at least 100,000, based on the number of proteins in our body. So clearly the interaction of that DNA with our body is a hell of a lot more complicated than we thought. So, to answer your question, I would say that we understand the function and structure of DNA extremely well, because those things are very simple. What is very, very complicated, and what we don't yet fully understand, is the myriad interactions between genes and the body, and between genes and other genes.

How do we know that there is not some method within the genome that is supposed to generate some level of variation--i.e., it's not random mutations but rather variation achieved through randomness generated purposefully by the code?

DNA accumulates copying errors because copying is never perfect; these errors are largely reduced by error-checking mechanisms in the replication process. But it isn't perfect, and so we know that mutation must occur.

Some organisms apparently can react to certain stresses by reducing the effectiveness of these error-checks; as a result the DNA mutates more often. We know that random mutation will always occur because of the second law of thermodynamics. There's no way to completely prevent it. If what you're asking is "can a cell allow certain areas of the DNA to mutate, and completely prevent other areas from doing so?" the answer appears to be "no". Some areas of DNA appear to mutate more frequently than others, but no area of DNA can be perfectly protected from mutation.

Is it possible that this junk DNA DOES perform some function

Biologists hate the term "junk DNA" because it causes precisely this confusion. The sequences you refer to are not transcribed, you are correct.

But that's not to say that they're without purpose. As I said earlier, it's impossible to prevent mutation, and a mutation is more likely to be harmful than to be helpful. Having the vast majority of your DNA be sequences that will never be transcribed may help "shield" valid genetic sequences from mutation by making it less likely that a random mutation will occur in the middle of a gene.

Moreover, junk DNA has an additional function. If you were a teacher, and you suspected two students had copied each others papers (and not just written two similar papers because they both researched the same topic), you would know if they had done so because both papers had the same spelling mistakes, grammatical errors, and typos. So too do these "plagerized errors" allow us to reconstruct evolutionary histories, because the only reason two species would have the same collection of errors and typos in their DNA is if they had copied their DNA from the same source - that is, they shared a common ancestor.

*If you'd like to help out, you can download and run the distributed "Folding @ Home" client, which uses your spare CPU cycles to run protein folding analysis.

http://folding.stanford.edu/

This message has been edited by crashfrog, 01-16-2005 13:10 AM


This message is a reply to:
 Message 1 by TheLiteralist, posted 01-16-2005 1:12 AM TheLiteralist has not yet responded

Replies to this message:
 Message 13 by Wounded King, posted 01-17-2005 10:01 AM crashfrog has responded
 Message 14 by NosyNed, posted 01-17-2005 10:12 AM crashfrog has responded

  
Wounded King
Member (Idle past 2136 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 13 of 98 (177792)
01-17-2005 10:01 AM
Reply to: Message 12 by crashfrog
01-16-2005 1:07 PM


The major surprise of the last few years was how simple our DNA really is, less than 25k genes. We had predicted at least 100,000, based on the number of proteins in our body.

Shouldn't this say 'how small our genome really is', since the genomic architecture coding for the protein complement, assuming our estimates for that number are reasonably accurrate, must be considerably more complex in this scenario than in the simplest scenario where every protein is coded for by a single gene.

We have a fairly solid grasp of the basic mechanisms of gene regulation and expression and can interpret a fair amount of the motifs and sequences important in these processes, but there are undoubtedly a number of finer levels the exact mechanisms of which are stil obscure. And the more compact than expected genome increases the importance of these mechanisms making the genomic picture more complex.

Moreover, junk DNA has an additional function. If you were a teacher, and you suspected two students had copied each others papers (and not just written two similar papers because they both researched the same topic), you would know if they had done so because both papers had the same spelling mistakes, grammatical errors, and typos. So too do these "plagerized errors" allow us to reconstruct evolutionary histories, because the only reason two species would have the same collection of errors and typos in their DNA is if they had copied their DNA from the same source - that is, they shared a common ancestor.

That isn't a function of junk DNA.

TTFN,

WK


This message is a reply to:
 Message 12 by crashfrog, posted 01-16-2005 1:07 PM crashfrog has responded

Replies to this message:
 Message 15 by crashfrog, posted 01-17-2005 12:06 PM Wounded King has not yet responded

    
NosyNed
Member
Posts: 8829
From: Canada
Joined: 04-04-2003
Member Rating: 4.5


Message 14 of 98 (177797)
01-17-2005 10:12 AM
Reply to: Message 12 by crashfrog
01-16-2005 1:07 PM


Shielding DNA
But that's not to say that they're without purpose. As I said earlier, it's impossible to prevent mutation, and a mutation is more likely to be harmful than to be helpful. Having the vast majority of your DNA be sequences that will never be transcribed may help "shield" valid genetic sequences from mutation by making it less likely that a random mutation will occur in the middle of a gene.

I don't see how you think this works. Just because some random mutation happens in the "junk" DNA doesn't mean it won't happen elsewhere in the DNA.

It sounds like you're saying that the odds of a mutation are such and such and if one happens here it is less likely it will happen there. But the odds are so many per million base pairs. So if the coding DNA is so many base pairs long then it's chances of a really random mutation are just as great no matter what has happened in the other millions of base pairs.


This message is a reply to:
 Message 12 by crashfrog, posted 01-16-2005 1:07 PM crashfrog has responded

Replies to this message:
 Message 16 by crashfrog, posted 01-17-2005 12:19 PM NosyNed has not yet responded

  
crashfrog
Inactive Member


Message 15 of 98 (177829)
01-17-2005 12:06 PM
Reply to: Message 13 by Wounded King
01-17-2005 10:01 AM


That isn't a function of junk DNA.

Technically, no, it's not. That wasn't meant to be a statement of fact, but rather, a segue into how junk DNA is employed in the lab, and how it holds up the evolutionary model. But I'm sorry that it was clumsy and easily misunderstood.


This message is a reply to:
 Message 13 by Wounded King, posted 01-17-2005 10:01 AM Wounded King has not yet responded

  
1
234567Next
Newer Topic | Older Topic
Jump to:


Copyright 2001-2018 by EvC Forum, All Rights Reserved

™ Version 4.0 Beta
Innovative software from Qwixotic © 2019