The whole greater than the sum of it's parts?

Cpt_pineapple
atheist
Cpt_pineapple's picture
Posts: 5492
Joined: 2007-04-12
User is offlineOffline
The whole greater than the sum of it's parts?

I'd like to take a little poll and ask do you think the whole is greater than a sum of it's parts?

 

That is basically, can we get more information studying the universe as a whole, or reducing it as far as we can?

 

 

This isn't really a debate topic, I'll probably just read the answers and not participate.

 

 

 

 

 


Kevin R Brown
Superfan
Kevin R Brown's picture
Posts: 3142
Joined: 2007-06-24
User is offlineOffline
...I don't really understand

...I don't really understand the question.

 

How does one study the universe 'as a whole' without studying it's components, given that the universe is entirely comprised of said components?

Quote:
"Natasha has just come up to the window from the courtyard and opened it wider so that the air may enter more freely into my room. I can see the bright green strip of grass beneath the wall, and the clear blue sky above the wall, and sunlight everywhere. Life is beautiful. Let the future generations cleanse it of all evil, oppression and violence, and enjoy it to the full."

- Leon Trotsky, Last Will & Testament
February 27, 1940


Wonderist
atheist
Wonderist's picture
Posts: 2479
Joined: 2006-03-19
User is offlineOffline
Umm, both? I'm both a

Umm, both? I'm both a reductionist and an emergentist. Not only is the whole greater than the sum of its parts, but the parts are greater than the sum of the whole. Eye-wink

Cities arise from buildings, but buildings are made of bricks. To choose only one or the other, reductionism vs. emergentism, would be to limit your perspective either to the small or to the large. I have found that most people who profess proudly, "But the whole is greater than the sum of its parts!" don't really see that that leaves them without a foundation. They propose empty ideas like 'spirit' and whatnot. Without the foundation of a physical substrate, these ideas are impotent. On the other hand, some (few, but some) naive materialists reject the obvious complexities of reality by focusing too much on the word 'just'. We are atoms, yes, but we are not 'just' atoms. We are atoms in a particular arrangement, with particular processes, which is stable through time, which means we are 'more' than 'just' atoms. So we are 'more' than the sum of our parts. But if we ignore the parts, and propose ideas like 'spirit', then actually the study of the parts themselves will reveal more understanding than speculation about bodiless spirits. So the parts are 'more' than the sum of the whole (in other words: the whole, when conceived without relation to its parts, teaches us less than the parts, when conceived without relation to the whole).

Wonderist on Facebook — Support the idea of wonderism by 'liking' the Wonderism page — or join the open Wonderism group to take part in the discussion!

Gnu Atheism Facebook group — All gnu-friendly RRS members welcome (including Luminon!) — Try something gnu!


Hambydammit
High Level DonorModeratorRRS Core Member
Hambydammit's picture
Posts: 8657
Joined: 2006-10-22
User is offlineOffline
 It's not an either/or

 It's not an either/or question.  Reductionism isn't about simplifying.  It's about building complexity.  Put simply, as complexity increases, the probability of accurately predicting the next higher level becomes substantially (sometimes exponentially) worse.  In other words, if we have a few carbon atoms and a couple of oxygen atoms, there's a relatively limited number of possible combinations.  However, as we move up to the level of amino acids or proteins, we find that accurate prediction from the ground up becomes next to impossible.

The answer to the problem is beginning at the macro level and looking for patterns.  We look at the "whole" and try to make guesses as to the constituent "parts."  When we find those parts, we repeat the same process, as far down as we can go, moving from complex to simple.  As we do this, we discover the principles which govern each "level."  As we find consistency in theory, we gain the ability to make predictions about new complex systems.

So, to answer your question directly, yes, we must start at the macro level, for we cannot hope to build a universe from subatomic particles.  (How would we know about them if we hadn't started at our level of observation?)  The quest for knowledge must begin at the observational level, which, by virtue of our limited senses, is necessarily confined to "wholes."  Once we have used our observation of wholes to determine the constituent parts, we can learn (through indirect observation) far more through reductionism (building complexity) than we could know from direct observation alone.

And as for the sum of the parts being greater than the whole, it's really a matter of philosophy more than fact.  Sure, there are emergent systems, but even those are a matter of perspective.  We think of our "minds" as being greater than the sum of atoms because we think of our minds as having value.  Then again, if you look at a carbon molecule and then a diamond (or graphite), you can say the same thing.  It seems odd to us to think of diamonds as anything "emergent" because they don't "do" anything, but our brains only "do" something from the perspective of our own sense of purpose, which is just a product of the interaction of atoms.

In the end, it's all atoms.

Oh, and while I'm thinking about it, (deludedgod may correct me on some details here) the information contained in a gene specifies how a protein will be built, but proteins fold from two into three dimensions, and the information for the three dimensions is "added" to the information contained in the gene itself.  In other words, genes don't actually contain enough information to specify the complete information content of the organism they are building.  While we are tempted to say that the sum of the organism is more information than the information contained in its parts, that information didn't come from nowhere.  It was present in the environment, which interacted with the genes to complete the construction of the organism.

 

Atheism isn't a lot like religion at all. Unless by "religion" you mean "not religion". --Ciarin

http://hambydammit.wordpress.com/
Books about atheism


BobSpence
High Level DonorRational VIP!ScientistWebsite Admin
BobSpence's picture
Posts: 5939
Joined: 2006-02-14
User is offlineOffline
I pretty much agree with

I pretty much agree with Hamby.

I might just add some of the other ways of thinking about this 'whole vs. parts' thing.

Groups of Interacting, connected simple components can frequently display properties which cannot sensibly be displayed by the individual bits which make them up. That's pretty much a no-brainer; any function which requires more than one atom cannot be achieved with a single atom.

At a very elementary level, separate piles of sand, cement, and gravel, and a supply of water, cannot be used as is to construct a building, they have to be combined into concrete, which still has essentially the same set of atoms, yet dramatically different physical properties.

You can't access the internet on a pile of unconnected semiconductor chips, circuit boards, wires, etc, even if you have all the same set of bits that a computer is constructed of.

So of course the whole can easily be more, in at least some sense, than the sum of its parts, that is a utterly undeniable. Even if the whole is not clearly 'more', it will almost certainly be an entirely different sort of entity, assuming the 'parts' are actually closely linked to each other in some way beyond simply being in the same disorganised heap.

And of course, as Hamby says, you have to study both the properties of the parts and the way they interact in the composite entity, and how the capabilities and attributes of the 'whole' emerge from the 'parts'. Only a philosopher could generate some pointless argument about the 'whole' being in some way 'just' the sum of its parts. If you want to extend the mathematical idea, maybe something between the 'sum' and the 'product' (as in multiplication) of its parts would be more accurate, depending how they the parts are organized into the 'whole'.

A primary reason why we run into this 'problem' is that even though in principle the ultimate properties of the highest level organised structures are inherent in the simple properties of the ultimate particles and the 'laws' which describe the way they interact, we are totally incapable of analysing the behaviour of more than small numbers of particles without first understanding the systematic behaviour of larger common aggregates, such as atoms, then analysing the behaviour of groups of atoms. When the number of atoms get too large, we have to step back further and think in terms of molecules.

This is simply due to the rapid increase in the possible ways a group of even identical simple entities can interact in systematic and unexpected ways as the numbers involved increase.

And so on, all the way up to living organisms, civilizations, solar systems and galaxies...

Arguing about the 'whole' and 'the sum of its parts' is something only the philosophically inclined waste any time on, AFAICS.

Favorite oxymorons: Gospel Truth, Rational Supernaturalist, Business Ethics, Christian Morality

"Theology is now little more than a branch of human ignorance. Indeed, it is ignorance with wings." - Sam Harris

The path to Truth lies via careful study of reality, not the dreams of our fallible minds - me

From the sublime to the ridiculous: Science -> Philosophy -> Theology


deludedgod
Rational VIP!ScientistDeluded God
deludedgod's picture
Posts: 3221
Joined: 2007-01-28
User is offlineOffline
Quote:deludedgod may correct

Quote:

deludedgod may correct me on some details here

It is not the details. The whole statement is completely wrong. The 3D structure of a protein is completely specified by its amino acid sequence and hence by the DNA sequence which corresponds to it. If this were not the case, then DNA would be completely useless as a molecule. This is elucidated very precisely by me here.

The Third Revolution

 

No information is "added" in order to create a folded, functional protein. At least not usually (there are proteins called hsp-chaperones which aid in the formation of some proteins and respond to heat damage which can cause malformation, but that's a technical matter. Proteins fold solely on the basis of their sequence. If this were not the case, biological life would not exist.

 

 

"Physical reality” isn’t some arbitrary demarcation. It is defined in terms of what we can systematically investigate, directly or not, by means of our senses. It is preposterous to assert that the process of systematic scientific reasoning arbitrarily excludes “non-physical explanations” because the very notion of “non-physical explanation” is contradictory.

-Me

Books about atheism


Renee Obsidianwords
High Level DonorModeratorRRS local affiliate
Renee Obsidianwords's picture
Posts: 1388
Joined: 2007-03-29
User is offlineOffline
This reminds me of a team

This reminds me of a team building exercise I facilitated a few years back. . . . .  "each individual is part of the whole team"   

 

Slowly building a blog at ~

http://obsidianwords.wordpress.com/


Hambydammit
High Level DonorModeratorRRS Core Member
Hambydammit's picture
Posts: 8657
Joined: 2006-10-22
User is offlineOffline
 Quote:It is not the

 

Quote:
It is not the details. The whole statement is completely wrong. The 3D structure of a protein is completely specified by its amino acid sequence and hence by the DNA sequence which corresponds to it. If this were not the case, then DNA would be completely useless as a molecule. This is elucidated very precisely by me here.

The Third Revolution

Well, shit.  I hate when I'm totally wrong.  Now I have to remember which author I'm mad at for giving me that idea.

Quote:
Proteins fold solely on the basis of their sequence. If this were not the case, biological life would not exist.

Got it.  Thanks.

 

 

Atheism isn't a lot like religion at all. Unless by "religion" you mean "not religion". --Ciarin

http://hambydammit.wordpress.com/
Books about atheism


Hambydammit
High Level DonorModeratorRRS Core Member
Hambydammit's picture
Posts: 8657
Joined: 2006-10-22
User is offlineOffline
 Oh, and Pineapple, add

 Oh, and Pineapple, add this to your list of times I've been wrong and admitted it.

Thanks so much.

 

Atheism isn't a lot like religion at all. Unless by "religion" you mean "not religion". --Ciarin

http://hambydammit.wordpress.com/
Books about atheism


Wonderist
atheist
Wonderist's picture
Posts: 2479
Joined: 2006-03-19
User is offlineOffline
deludedgod wrote:It is not

deludedgod wrote:

It is not the details. The whole statement is completely wrong. The 3D structure of a protein is completely specified by its amino acid sequence and hence by the DNA sequence which corresponds to it. If this were not the case, then DNA would be completely useless as a molecule. This is elucidated very precisely by me here.

The Third Revolution

 

No information is "added" in order to create a folded, functional protein. At least not usually (there are proteins called hsp-chaperones which aid in the formation of some proteins and respond to heat damage which can cause malformation, but that's a technical matter. Proteins fold solely on the basis of their sequence. If this were not the case, biological life would not exist.

Wow, I get to correct DG! Cool. Eye-wink

Actually, there are other factors, which I'm sure you mentioned in your article, which affect the folding of amino acid sequences, such as temperature, pH levels, presence of various mineral co-factors, etc. If you put the same amino acid sequence in a highly acidic or highly basic solution, it will unfold, or fold differently. That is an example of what Hamby was talking about when he said the environment provides additional information.

In fact, if it were really true that DNA completely specified 3D structure without any input from the environment, then proteins could not function as enzymes, because their action as enzymes depends on them changing their 3D shape in response to the presence of substrate, which is an environmental piece of information. Same sequence, different shape, depending on the environment.

Wonderist on Facebook — Support the idea of wonderism by 'liking' the Wonderism page — or join the open Wonderism group to take part in the discussion!

Gnu Atheism Facebook group — All gnu-friendly RRS members welcome (including Luminon!) — Try something gnu!


Vastet
atheistBloggerSuperfan
Vastet's picture
Posts: 13210
Joined: 2006-12-25
User is offlineOffline
Cpt_pineapple wrote:I'd like

Cpt_pineapple wrote:

I'd like to take a little poll and ask do you think the whole is greater than a sum of it's parts?

That is basically, can we get more information studying the universe as a whole, or reducing it as far as we can?

This isn't really a debate topic, I'll probably just read the answers and not participate.

I think that the whole is incapable of being greater* than the sum of its parts, and vice versa. The whole is its parts, and the parts make the whole. They are inseperable. 

*Greater does not seem to be a good term to utilize here. More would be a preffered term, as greater implies that something is better than something else. Being "better" would require subjective input, so the terminology doesn't fly for a question. More might also be subject to this, but it seems less likely to in my eyes.

 

Re: Protein folding....

*Grabs popcorn and waits patiently for this interesting side topic to resolve itself*

Proud Canadian, Enlightened Atheist, Gaming God.


Kevin R Brown
Superfan
Kevin R Brown's picture
Posts: 3142
Joined: 2007-06-24
User is offlineOffline
Quote:That is an example of

Quote:
That is an example of what Hamby was talking about when he said the environment provides additional information.

*Narrows eyes*

 

...Am I the only person who has grown to despise the terms, 'additional information' and 'new information'?

I mean, are those terms ever even used within academic circles? It's so vague and sloppy-sounding.

Quote:
"Natasha has just come up to the window from the courtyard and opened it wider so that the air may enter more freely into my room. I can see the bright green strip of grass beneath the wall, and the clear blue sky above the wall, and sunlight everywhere. Life is beautiful. Let the future generations cleanse it of all evil, oppression and violence, and enjoy it to the full."

- Leon Trotsky, Last Will & Testament
February 27, 1940


Hambydammit
High Level DonorModeratorRRS Core Member
Hambydammit's picture
Posts: 8657
Joined: 2006-10-22
User is offlineOffline
 Quote:...Am I the only

 

Quote:
...Am I the only person who has grown to despise the terms, 'additional information' and 'new information'?

Possibly...

Quote:
I mean, are those terms ever even used within academic circles? It's so vague and sloppy-sounding.

Most definitely.  Information theory is a big part of science, and has a lot to do with biology.  Richard Dawkins is a big fan.

By the way, here's where I got my information.  (It took a couple of hours of digging to remember where I'd read it.)

Monod wrote:
Thus there is a seeming contradiction between the statement that the genome 'entirely defines' the function of a protein and the fact that the function is linked to a three-dimensional structure whose data content is richer than the direct contribution made to the structure by the genome.

Monod, Jacques. 1971. Chance and Necessity. New Yor: Knopf.  Vintage Paperback, p. 94

This paragraph is cited in Darwin's Dangerous Idea on p. 196

 

 

Atheism isn't a lot like religion at all. Unless by "religion" you mean "not religion". --Ciarin

http://hambydammit.wordpress.com/
Books about atheism


Wonderist
atheist
Wonderist's picture
Posts: 2479
Joined: 2006-03-19
User is offlineOffline
Vastet wrote:*Greater does

Vastet wrote:

*Greater does not seem to be a good term to utilize here. More would be a preffered term, as greater implies that something is better than something else. Being "better" would require subjective input, so the terminology doesn't fly for a question. More might also be subject to this, but it seems less likely to in my eyes.

When I use 'more' or 'greater' in this context, I mean 'able to make more accurate predictions'. If we try to predict what someone will do based on our knowledge of their atoms, then we will fail miserably. But if we use our concept of 'mind', and our study of psychology, we may be able to make more than mere random predictions. Therefore, the concept of 'mind' is 'more' than the concept of the atoms that make up the mind, because using this concept allows us to make better predictions than if we did not have the concept.

Even if we start with the concept of atoms, and we 'build up' from there, eventually we will have to develop new concepts to denote various 'built up' structures of atoms. These new concepts are required because they allow us to make better predictions than if we did not use the concepts.

So, while they are 'abstractions' in the sense that they try to conceptualize a more complex phenomenon, they are also 'real' in the sense that they *do* allow us to make better predictions.

For example, an 'atom' itself is 'just' electrons, protons, and neutrons. But yet we speak of atoms as if they have an independent existence. And in some sense they do, because the atom theory allows us to make better predictions than if we did not have the concept of atoms. Likewise, protons and neutrons are 'just' quarks, which are 'just' wave-functions, etc. But when we try to explain macro-level phenomena in terms of wave-functions, we quickly run into a brick wall. 

Wonderist on Facebook — Support the idea of wonderism by 'liking' the Wonderism page — or join the open Wonderism group to take part in the discussion!

Gnu Atheism Facebook group — All gnu-friendly RRS members welcome (including Luminon!) — Try something gnu!


deludedgod
Rational VIP!ScientistDeluded God
deludedgod's picture
Posts: 3221
Joined: 2007-01-28
User is offlineOffline
I wouldn't have considered

I wouldn't have considered what natural cited as "additional information" because (a) temperature is constant in the cell and (b) For proteins which require certain pH to function such as those in lysosomes, their ability to shift into their functional conformation when the pH alters is a consequence of their sequence and (c) the ability of proteins to respond allosterically to certain coenzymes and ligands to produce certain functional alterations is again, a consequence of their sequence. These facts are crucial to the functioning of cells. For example, in the central process of protein translocation, for proteins to be imported into membrane bound organelles which are topologically distinct requires them to unfold as the polypeptide chain is passed through, and refold again on the other side. I was thinking more about the heat-shock pathways in which the hsp chaperons detect malformed proteins and refold them, and if they are irreperable, to reject them into the proteolysis pathway. Also, one could argue that the actual conditions specific proteins need to fold are created by other proteins as a consequence of their function which is a consequence of their sequence and their transcription pattern which depends on the presence of GRP which is again a consequence of their sequence. For proteins which must enter membrane bound organelles which are pH specific, those specific pH values are maintained by H+ pumps, which have that function on the basis of their sequence and are present in the cell due to the activity of gene regulatory proteins which is again, due to their sequence. Likewise for allosteric alterations, and the presence of coenzymes altering the function of proteins by mechanically induced structural alternations such as retinal in rhodopsin, their regulation and (except for those that come from the diet) their presence is ultimately a consequence of enzyme pathways and therefore, the activity of those proteins requiring them is determined by other proteins whose activity in turn...um, well you see where I'm going with this.

Quote:

1971

1971? Jesus, no wonder its wrong. This discipline didn't even exist back then.

 

Quote:

whose data content is richer than the direct contribution made to the structure by the genome.

This is garbage. Firstly, this is too vague to be meaningful. No serious academic circle would accept a statement involving the phrase "data content of a protein" and they certainly wouldn't accept the phrase "richer" which means nothing.Secondly, the "direct contribution" made to the structure of a protein by the genome is the sequence. Even in 1971, that was known. It was elucidated by Watson in 1958! The sequence determines the structure. The latter statement has been experimentally verified. You can verify it yourself if you want. Take a solution of catalase and add hydrogen peroxide (the substrate) and hook it up to a gas syringe. You'll see gas being given off. That's the oxygen from the decomposition reaction. Take a malforming agent like concentrated sodium hydroxide and add a known amount, which will cause the protein to spontaneously unfold. Now add hydrogen peroxide. No more gas. Now titrate in hydrochloric acid until the endpoint is reached. Add the susbtrate again. The reaction proceeds. Once the malforming agent has been neutralized, the protein spontaneously refolds in vitro. That's it. You've just demonstrated that all the information needed to create the functional 3D structure is contained in the sequence which is contained in the genome.

 

"Physical reality” isn’t some arbitrary demarcation. It is defined in terms of what we can systematically investigate, directly or not, by means of our senses. It is preposterous to assert that the process of systematic scientific reasoning arbitrarily excludes “non-physical explanations” because the very notion of “non-physical explanation” is contradictory.

-Me

Books about atheism


Wonderist
atheist
Wonderist's picture
Posts: 2479
Joined: 2006-03-19
User is offlineOffline
Kevin R Brown

Kevin R Brown wrote:

Quote:
That is an example of what Hamby was talking about when he said the environment provides additional information.

*Narrows eyes*

 

...Am I the only person who has grown to despise the terms, 'additional information' and 'new information'?

I mean, are those terms ever even used within academic circles? It's so vague and sloppy-sounding.

First, I come from a background of computer science, where talk of 'more' and 'additional' information is so basic as to be considered a "Yeah, and?" kind of concept.

To encode an integer in the range of 0 to 65535 requires more (twice as much) information as to encode an integer in the range of 0 to 255. This is a no-brainer.

My laptop can hold about 900 times more information than my first desktop computer could on its harddrive.

The human genome holds 'less' information than many plant genomes.

From a physics point of view, the argument is not so clear cut. However, information theorists in physics do have more-or-less working definitions of 'information', and they do discuss 'more' and 'additional' information.

If we look at Einstein's relativity, for instance, we already have the concept of information showing up, when Einstein discusses simultaneity, causality, and communication. We have the concept of the 'speed' of information, which is, not coincidentally, the speed of light.

Yes, information is quantifiable, and can be compared in terms of quantity.

Wonderist on Facebook — Support the idea of wonderism by 'liking' the Wonderism page — or join the open Wonderism group to take part in the discussion!

Gnu Atheism Facebook group — All gnu-friendly RRS members welcome (including Luminon!) — Try something gnu!


deludedgod
Rational VIP!ScientistDeluded God
deludedgod's picture
Posts: 3221
Joined: 2007-01-28
User is offlineOffline
Quote:The human genome holds

Quote:

The human genome holds 'less' information than many plant genomes.

No it doesn't. In terms of protein encoding (which is a rough gauge of biological complexity, I say "rough" because of things like alternative splicing) the human genome is the most complex, with 30,000 proteins and holds more "information" in the sense that it contains a greater amount of sequence directly responsible for the encoding of amino acid sequences and more complex regulatory regions. It's true that many plant genomes have more base pairs than human genomes but we never talk about Eukaryotic genomes in terms of number of base pairs because it has no correlation with biological complexity. Actually, we never use the term "information". We talk about coding regions, regulatory regions, STR regions, etc. but never "information".

"Physical reality” isn’t some arbitrary demarcation. It is defined in terms of what we can systematically investigate, directly or not, by means of our senses. It is preposterous to assert that the process of systematic scientific reasoning arbitrarily excludes “non-physical explanations” because the very notion of “non-physical explanation” is contradictory.

-Me

Books about atheism


BobSpence
High Level DonorRational VIP!ScientistWebsite Admin
BobSpence's picture
Posts: 5939
Joined: 2006-02-14
User is offlineOffline
Vastet wrote:Cpt_pineapple

Vastet wrote:

Cpt_pineapple wrote:

I'd like to take a little poll and ask do you think the whole is greater than a sum of it's parts?

That is basically, can we get more information studying the universe as a whole, or reducing it as far as we can?

This isn't really a debate topic, I'll probably just read the answers and not participate.

I think that the whole is incapable of being greater* than the sum of its parts, and vice versa. The whole is its parts, and the parts make the whole. They are inseperable. 

*Greater does not seem to be a good term to utilize here. More would be a preffered term, as greater implies that something is better than something else. Being "better" would require subjective input, so the terminology doesn't fly for a question. More might also be subject to this, but it seems less likely to in my eyes.

Re: Protein folding....

*Grabs popcorn and waits patiently for this interesting side topic to resolve itself*

Any given set of 'parts' can typically be assembled in many different composite 'wholes', which are typically very different in form and function, so there is no way the 'whole' can be the same as the 'sum of its parts'.

Now as to the use of 'more' or 'greater', I understand the objection, if the terms are being applied in some value-laden sense. However, composite objects do have more attributes, properties, whatever, do require more data to describe them - you have to include the way the parts are connected to each other, their relative position, etc - so even at a simple descriptive level, there is normally 'more' to them.

I might add I also have almost a lifetime of experience in computer programming, so it gives me a similar perspectives on 'information' to Natural.

It's funny, but 'greater' is the standard computer programming term for expressing that one number is larger than another, IOW the most reductionist way to compare two things.

Favorite oxymorons: Gospel Truth, Rational Supernaturalist, Business Ethics, Christian Morality

"Theology is now little more than a branch of human ignorance. Indeed, it is ignorance with wings." - Sam Harris

The path to Truth lies via careful study of reality, not the dreams of our fallible minds - me

From the sublime to the ridiculous: Science -> Philosophy -> Theology


BobSpence
High Level DonorRational VIP!ScientistWebsite Admin
BobSpence's picture
Posts: 5939
Joined: 2006-02-14
User is offlineOffline
deludedgod wrote:Quote:The

deludedgod wrote:

Quote:

The human genome holds 'less' information than many plant genomes.

No it doesn't. In terms of protein encoding (which is a rough gauge of biological complexity, I say "rough" because of things like alternative splicing) the human genome is the most complex, with 30,000 proteins and holds more "information" in the sense that it contains a greater amount of sequence directly responsible for the encoding of amino acid sequences and more complex regulatory regions. It's true that many plant genomes have more base pairs than human genomes but we never talk about Eukaryotic genomes in terms of number of base pairs because it has no correlation with biological complexity. Actually, we never use the term "information". We talk about coding regions, regulatory regions, STR regions, etc. but never "information".

It would still be true to say that a longer genome may have more information content, using the simplest measure of information content, namely the shortest number of bytes which could encode the sequence of base-pairs using the most efficient compression possible. This would depend on both the number of base-pairs and the amount of repetition and redundancy in general, eg a run of 2000 identical base-pairs could be described by no more than 14 bits, ie no more than two ASCII characters. This assumes a simple run-length compression scheme.

If we are describing a genome by the number of active encoding sites, then yes that would be a more meaningful measure, at least according to the assumption that non-coding or 'junk' DNA regions have no utility at all.

This begs the question to an extent, since there are hypotheses, and some indicative studies, that they may serve some use, perhaps as a repository of 'dormant' genes which some mutation or relocation could activate and serve as a potential new step in evolution. Or perhaps some other regulatory function, or structural purpose. So maybe some allowance should be made for these regions. It would be exceedingly hard, perhaps futile, to quantify this in hard measures of 'information content'.

Assessing information content of such real-world structures is somewhat fuzzy, but we can usually put useful upper and lower bounds on it. The length of a lossless compressed bit-sequence which could encode the raw sequence would be set an upper bound. The number of unique functional proteins would define a lower bound.

Favorite oxymorons: Gospel Truth, Rational Supernaturalist, Business Ethics, Christian Morality

"Theology is now little more than a branch of human ignorance. Indeed, it is ignorance with wings." - Sam Harris

The path to Truth lies via careful study of reality, not the dreams of our fallible minds - me

From the sublime to the ridiculous: Science -> Philosophy -> Theology


Vastet
atheistBloggerSuperfan
Vastet's picture
Posts: 13210
Joined: 2006-12-25
User is offlineOffline
Perhaps it would clear

Perhaps it would clear things up a bit if I informed people that the post I wrote was utilizing the context of the universe as the "whole", and everything within it as the "part(s)". In this context, rearranging the part(s) does nothing to affect the whole, just within the system of part(s) being changed. For example: The universe would still be the universe if Earth and Jupiter were to switch positions.

If that doesn't help, then I don't think I'm going to be able to explain my post sufficiently to argue the point. Sticking out tongue

Proud Canadian, Enlightened Atheist, Gaming God.


deludedgod
Rational VIP!ScientistDeluded God
deludedgod's picture
Posts: 3221
Joined: 2007-01-28
User is offlineOffline
Quote:If we are describing a

Quote:

If we are describing a genome by the number of active encoding sites, then yes that would be a more meaningful measure, at least according to the assumption that non-coding or 'junk' DNA regions have no utility at all.

This is why the subject is so difficult to assess, and in fact why biologists in general shy away from these terms. Yes, we can define DNA as a three-bit base-four system because in terms of digital-to-digital conversion (a sequence of nucleotides to a sequence of amino acids) that's what it is. But because storage of amino acid sequences by DNA is an active process (in the sense that the process of digital conversion is under the control of the very products of the encoding process) it is difficult to assess the biological complexity that could arise solely on the basis of this criteria. Ultimately, whereas the DNA encoding process is a digital to digital conversion process, the actual process of specification of the current state of the cell by how the cell responds to its external signals and internal regulation, both of which are determined by the genome, is an analogue process (that is, possible states are continuous, and are defined by the expression pattern of the genome) the process by which the actual digital encoding process is controlled by the very products of that process is an example of digital-to-analogue conversion. That was exactly what was elucidated by me in the link above. So, instead of discussing DNA purely in terms of the number of base pairs (which is not actually meaningful anyway since the system of three-bit base-four encoding applies only to exons, which make up a tiny fraction of the genome itself, and only sequences which have functioning promoter regions could possibly be transcribed anyway) we should gauge the process by the complexity of the combinatorial control of gene expression and protein regulation which allows for the complexity of eukaryota in the first place. The easiest way to do this is to look at the number of coding sequences because we can then roughly assess the extensiveness of the gene regulatory network. The other way is to look at the complexity of the regulatory motifs that lie in the promotor regions of various genes.

"Physical reality” isn’t some arbitrary demarcation. It is defined in terms of what we can systematically investigate, directly or not, by means of our senses. It is preposterous to assert that the process of systematic scientific reasoning arbitrarily excludes “non-physical explanations” because the very notion of “non-physical explanation” is contradictory.

-Me

Books about atheism


Hambydammit
High Level DonorModeratorRRS Core Member
Hambydammit's picture
Posts: 8657
Joined: 2006-10-22
User is offlineOffline
 By the way, I'm just

 By the way, I'm just watching the festivities at this point.  I don't have a horse in the race.  I only cited my source to prove that I wasn't making shit up.  I wrote that little bit of the post as an afterthought from memory.  Had I known my source was 1971, I'd have left it out of the post entirely.  In any case, I am very interested in this topic, but will be a spectator.

 

Atheism isn't a lot like religion at all. Unless by "religion" you mean "not religion". --Ciarin

http://hambydammit.wordpress.com/
Books about atheism


Wonderist
atheist
Wonderist's picture
Posts: 2479
Joined: 2006-03-19
User is offlineOffline
deludedgod wrote:Quote:The

deludedgod wrote:

Quote:

The human genome holds 'less' information than many plant genomes.

No it doesn't. In terms of protein encoding (which is a rough gauge of biological complexity, I say "rough" because of things like alternative splicing) the human genome is the most complex, with 30,000 proteins and holds more "information" in the sense that it contains a greater amount of sequence directly responsible for the encoding of amino acid sequences and more complex regulatory regions.

First of all, that's not the definition of 'information' I was using. I would use the compressed size of the base pair sequence. In other words, how many bits would be used to store it on a computer. This is roughly approximate to Kolmogorov's measure of information.

Second, regardless whether measured by base pairs or protein coding regions, it is still true that there are many plants with more protein encoding regions than humans. For example, rice have approx. 51,000 protein coding regions, according to here.

Third, when you get into alternative splicing, you are now talking about proteome complexity, not genome complexity. Small amounts of information (genome) can give rise to much greater amounts of information (proteome) via processing (such as transcription and splicing). However, that does not contradict the fact that the initial source of complexity (genome) has a small amount of information to start with.

The very simple equation zn+1 = zn2 + c of the Mandelbrot set can generate an infinite amount of information, simply by algorithmically following the progression for various starting c values. However, the equation itself can be represented by fewer than a couple dozen bytes. The equation itself has very little information in it.

Likewise with DNA. It gives rise to great complexity and vast information, but a human genome itself can be stored on a single 700 megabyte CD (approximately). If compressed, it could likely be stored in a few dozen megabytes, since it contains a lot of redundant sequences which are easily compressable using standard compression algorithms, such as Zip.

Quote:
It's true that many plant genomes have more base pairs than human genomes but we never talk about Eukaryotic genomes in terms of number of base pairs because it has no correlation with biological complexity. Actually, we never use the term "information". We talk about coding regions, regulatory regions, STR regions, etc. but never "information".

Frankly, it's irrelevant what terms you use in your field. *I* was talking about information in the genome, not biological complexity, coding regions, or any other thing. You're changing the subject by bringing in these other ideas which do not, in fact, contradict my point.

Wonderist on Facebook — Support the idea of wonderism by 'liking' the Wonderism page — or join the open Wonderism group to take part in the discussion!

Gnu Atheism Facebook group — All gnu-friendly RRS members welcome (including Luminon!) — Try something gnu!


deludedgod
Rational VIP!ScientistDeluded God
deludedgod's picture
Posts: 3221
Joined: 2007-01-28
User is offlineOffline
Quote:Second, regardless

Quote:

Second, regardless whether measured by base pairs or protein coding regions, it is still true that there are many plants with more protein encoding regions than humans. For example, rice have approx. 51,000 protein coding regions, according to here.

And most of those are retrotransposons. The same with other eukaryota with large numbers of coding regions with no known function. When assessing sets of genes, look for the expressed sequence tags to identify the transcipts. It's the number of proteins that matter.  Some genomes have more sequences than proteins. In contrast, the human genome has 25,000 coding sequences but 30,000 proteins, and it is for that reason that humans are the most biologically complex.

Since we aren't actually arguing about anything (we're talking past each other) we might as well stop. Now that I know the definition of information you are employing, I agree with you entirely.  Having studied in depth the process of combinatorial control, it just seems so obvious to me that you can generate a highly complex set of possible biological states from a small set of sequences that it is somewhat a "yeah, so" among molecular biologists.

"Physical reality” isn’t some arbitrary demarcation. It is defined in terms of what we can systematically investigate, directly or not, by means of our senses. It is preposterous to assert that the process of systematic scientific reasoning arbitrarily excludes “non-physical explanations” because the very notion of “non-physical explanation” is contradictory.

-Me

Books about atheism


Wonderist
atheist
Wonderist's picture
Posts: 2479
Joined: 2006-03-19
User is offlineOffline
deludedgod wrote:And most of

deludedgod wrote:
And most of those are retrotransposons. The same with other eukaryota with large numbers of coding regions with no known function. When assessing sets of genes, look for the expressed sequence tags to identify the transcipts. It's the number of proteins that matter.  Some genomes have more sequences than proteins. In contrast, the human genome has 25,000 coding sequences but 30,000 proteins, and it is for that reason that humans are the most biologically complex.

Just out of curiosity, do you have a link to a source that unambiguously shows that humans are more biologically complex (in terms of intracellular contents) than other eukaryotes? I'm not talking about brain complexity, but cellular complexity.

Wonderist on Facebook — Support the idea of wonderism by 'liking' the Wonderism page — or join the open Wonderism group to take part in the discussion!

Gnu Atheism Facebook group — All gnu-friendly RRS members welcome (including Luminon!) — Try something gnu!


deludedgod
Rational VIP!ScientistDeluded God
deludedgod's picture
Posts: 3221
Joined: 2007-01-28
User is offlineOffline
 Quote: Just out of

 

Quote:

Just out of curiosity, do you have a link to a source that unambiguously shows that humans are more biologically complex

I don't think the matter is unambiguous to begin with, but as humans have the largest network of gene regulatory proteins, the opportunity for the creation of complex regulatory patterns is greatest. It is thought that the modularity of gene regulation is a major driving force behind the evolution of multicellular Eukaryota.

The definitive authority on this matter is Molecular Biology of the Cell, currently in its 5th edition, so I consulted that. Here's what MBOC had to say:

MBOC wrote:

As might be expected, a correlation exists between the complexity of an organism and the number of genes in its genome (see Table 1-1). For example, total gene numbers range from less than 500 for simple bacteria to about 30,000 for humans

 

The number of genes is only very roughly correlated with the phenotypic complexity of an organism. Thus, for example, current estimates of gene number are 6,000 for the yeast Saccharomyces cerevisiae, 18,000 for the nematode Caenorhabditis elegans, 13,000 for Drosophila melanogaster, and 30,000 for humans (see Table 1-1). As we shall soon see, much of the increase in gene number with increasing biological complexity involves the expansion of families of closely related genes, an observation that establishes gene duplication and divergence as major evolutionary processes. Indeed, it is likely that all present-day genes are descendants—via the processes of duplication, divergence, and reassortment of gene segments—of a few ancestral genes that existed in early life forms.

In general, the more complex the organism, the larger its genome, but because of differences in the amount of excess DNA, the relationship is not systematic (see Figure 1-38). For example, the human genome is 200 times larger than that of the yeast S. cerevisiae, but 30 times smaller than that of some plants and amphibians and 200 times smaller than a species of amoeba. Moreover, because of differences in the amount of excess DNA, the genomes of similar organisms (bony fish, for example) can vary several hundredfold in their DNA content, even though they contain roughly the same number of genes. Whatever the excess DNA may do, it seems clear that it is not a great handicap for a higher eucaryotic cell to carry a large amount of it.

 

"Physical reality” isn’t some arbitrary demarcation. It is defined in terms of what we can systematically investigate, directly or not, by means of our senses. It is preposterous to assert that the process of systematic scientific reasoning arbitrarily excludes “non-physical explanations” because the very notion of “non-physical explanation” is contradictory.

-Me

Books about atheism


peppermint
Superfan
peppermint's picture
Posts: 539
Joined: 2006-08-14
User is offlineOffline
Well, you have to study BOTH

Well, you have to study BOTH "aspects" of the universe to understand it. Though I do think we can discover a lot by looking more considerably at "small" things.

*Our world is far more complex than the rigid structure we want to assign to it, and we will probably never fully understand it.*

"Those believers who are sophisticated enough to understand the paradox have found exciting ways to bend logic into pretzel shapes in order to defend the indefensible." - Hamby


spike.barnett
Superfan
spike.barnett's picture
Posts: 1018
Joined: 2008-10-24
User is offlineOffline
I think it's all about

I think it's all about scope. You have to pick a part of the universe and then reduce it into parts. When you've reduced it into parts, you then reduce those parts into their parts. Only then can you effectively understand why it works the way it does. Many emergent properties rely on the same underlying processes and interactions but still vary widely. Knowing those underlying principles won't necessarily equip you to understand the principles of a much larger or different scope. We can learn a lot from just observing the universe at surface level, but if we want to be able to truly understand whats going on we have to reduce it.

IOW Understanding the four interactions will not give you a great understanding of photosynthesis. In order to understand a given part, you must study it at it's level and then reduce from there.

After eating an entire bull, a mountain lion felt so good he started roaring. He kept it up until a hunter came along and shot him.

The moral: When you're full of bull, keep your mouth shut.
MySpace


Stosis
Posts: 327
Joined: 2008-10-21
User is offlineOffline
Wow, I have to say I

Wow, I have to say I understand very little of what you guys are talking about, I think I'll just answer the original question for now.

Of course the sum is greater than its parts. I can't think of a time when it wouldn't be. It would be interesting if someone could write a conherent consession on this. The thing is that to truely understand the universe (or anything) we must study the parts, ideally reduced as far as possible, and then look at how the interactions create emergent properties. If we keep doing this we can build our knowledge from the ground level all the way up to, well, I suppose the universe in its entiretly.