Pregressive evolution?

[diggnate]

Hey guys,
I'm new to the board, but I've been reading up on the latest posts here, and instead of trying to jump into conversations already in progress (many of them drifting way off original topic), I decided to start a new topic.

First off, I'm a Christian, but am not a "creationist". I've come to accept (at least tentatively) some of the work of ID theorists such as Dembski, Behe, etc. However, as one who is dedicated to science, I'm not married to theories, as they are (by their very nature) falsifiable, therefore I have no reason, emotional or otherwise, to accept any scientific conclusion based on anything but the facts.

I generally accept the age of the universe/earth as best theorized by cosmologists and geologists, and accept the theory of natural selection as a mechanism for change in biological organisms.

I do, however, also take seriously the logical inadequacies of the best theories for the evolution of Irreducibly Complex features in biology, which I may discuss further in later threads.

Also, and this is my main concern presently, I have serious questions about the process by which natural selection works on in which to provide novel functionality to biological organisms. I think I read here that you guys don't consider Darwinian evolution to be a progressive process NECESSARILY, but that many times it is progressive.

My question is, what proof do you have that Darwinian evolution is an informationally positive process? Can you provide examples of net information gain simply by a series of random mutations, preserved by natural selection? Please let me know if I need to provide more details.

[diggnate]

A mutation of a gene means that some part of the old gene sequence is lost. The light sensitive skin cells replace the tougher skin. It is impossible to find any example of change without being able to point out that something else has been lost.

It's good to see you admit that "evolution" is, by definition, an negative, or at best neutral process.

Famine means there is a poor food environment which in turn means an information loss in the environment?

Information loss has nothing to do with the environment. The possession of function is not dependent on the use of the function. The propagation of that function is indeed dependent on the use, but not the possession. Your speaking in very relative terms. Net information gain is not measured by its usefulness, but by mathematical total. Its use couldn't be more irrelevant to its possession. You either have function (directly correlating to its genetic information), or you don't (lack of genetic cause).

So what information loss occurs when humans gained the ability to digest milk? ( Adult Milk Tolerance).

Are you serious? No offense, but have you read anything about HOW adult humans happen to be lactose tolerant?

No. There are self replicating molecules we call DNA or genes and these are causal agents, that cause the phenotype to take on certain appearances and traits.

Which is where the information content ultimately lies.

The information content of these traits is determined by the environment.

No, it either is or is not informationally rich. The environment is simply where the information is utilized. The information was there before it was ever introduced to the environment and certainly before it was sent through the selection filter.

Light sensitive skin cells on a cave dweller, will not allow the cave dweller to functionally interact with its environment in a more complex way. Thus this genetic mutation contains no information.

True, but not how you meant it to be. It contained no net information gains because it did not gain more function than it lost. Selection aside, information is information. Function is function, regardless of whether it is propagated.

You have to demonstrate how mutations across generations allows a phenotypes features and traits to adapt to its environment. Which is exactly what evolution theory sets out to do.

Agreed, but that is only when determining selection. Evolution does a fine job at helping organisms survive. It doesn't do so well at adding net function (if it does it at all).

But up slope evolution is a gain in complexity of the features of the phenotype

Wrong. How can you possible say that a beetle losing its wings is a net gain in functional complexity? That makes no sense at all unless you apply your relative information gain assertion, and even at that it still makes no sense.

Which is just adaptation to its environment.

and adaptations occur by net information loss every time, as stated at the top.

You are trying to add a further conceptual layer of information gain. Frankly a concept that is empty of meaning.

Me? You introduced the idea of environmental information. I want to keep it simple mathematical accumulation.

Ignore what? Complexity? Well that is Climbing Mount improbable.

How can you climb when each step either removes information or keeps the net information content the same? Why is it that each "beneficial" mutation you cite is one that actually renders the organism weaker as a result? That is not climbing, my friend. That's a stasis.

Information loss? That is relative to the analysis you are making.

you mean math? add or subtract information, or keep it the same. There aren't more choices than that.

As already said. Every change, in some respect, or at some level, can be argued to entail information loss.

explain this then:
The first organism to ever live on the earth must have had at least 500,000 base pairs to live (at least, that's the lowest number currently for any organism, the Mycoplasma genitalium). Humans have 2.3 billion. Somewhere along the way, there must have been a true net information gain. This doesn't even take into account the innumerable amounts of functions that humans possess. You can't get away from it. At some point along the evolutionary timeline, something had to gain more function than it lost, resulting in a net information gain. How?

[Goat]

explain this then:
The first organism to ever live on the earth must have had at least 500,000 base pairs to live (at least, that's the lowest number currently for any organism, the Mycoplasma genitalium). Humans have 2.3 billion. Somewhere along the way, there must have been a true net information gain. This doesn't even take into account the innumerable amounts of functions that humans possess. You can't get away from it. At some point along the evolutionary timeline, something had to gain more function than it lost, resulting in a net information gain. How?

Can you prove that statement 'the first ogranism must have had at least 500,000 base pairs'.

[QED]

explain this then:
The first organism to ever live on the earth must have had at least 500,000 base pairs to live (at least, that's the lowest number currently for any organism, the Mycoplasma genitalium). Humans have 2.3 billion. Somewhere along the way, there must have been a true net information gain. This doesn't even take into account the innumerable amounts of functions that humans possess. You can't get away from it. At some point along the evolutionary timeline, something had to gain more function than it lost, resulting in a net information gain. How?

Hello diggnate You've made your question very clear here and it's naturally reasonable to want to know what's responsible for all this apparently clever engineering we see in nature. The answer has been supplied but, unlike the majority of the specialists in the field, you find the answer unsatisfactory. OK, I can sympathize with that -- I don't trust specialists that much either

But this answer can be formulated in such a way that it can be put to the test -- and that's what I want to see before I'm happy with an explanation. Remember, Darwinian evolution describes a principle (after all, Darwin didn't know about the actual genetic mechanism in living things when he formulated it). So the principle is a general one that can be applied to any equivalent mechanism. That's what working principles are all about -- especially when they're easy to describe!

So now we can ask if we can see your "informationally positive gradient" coming out of any general mechanism that applies this principle. This would be interesting and useful in all sorts of ways because it would equate to an Automated Invention Machine that could churn out patentable inventions for us.

The fact that this has now been demonstrated tells me that the principle we're debating here is without a doubt capable of generating an "informationally positive gradient" -- generating designs worthy of patents by exploring and exploiting whatever the environment has to offer. Most significantly I note that these apparent designs avoid getting bogged down by deleterious mutations without depending on input from an intelligent being to assist in making appropriate design decisions. We can see that it gains its own knowledge from its interactions with its environment.

The conclusion then is that the principle of Darwinian evolution can be shown to deliver the magic ingredient that many feel must be missing -- namely a source of creativity.

[diggnate]

Can you prove that statement 'the first ogranism must have had at least 500,000 base pairs'.

Unless you've got some inventive idea as to how an organism could spontaneously sequence MORE than half a million base pairs into functional DNA, then you have to assume the simplest organism was first. You could, I assume, claim that the organism had less than half a million BPs, but that would further prove my point.

I recommend reading up on any reputable abiogenesis research. They make the claims, not me. Unless of course, you think that the first organism contained 2.3+ billion base pairs too, and just degeneratively evolved over the last 3 billion years. Of course, that would mean the "tree of life" is upside down, and would also answer my question about evolution being a progressive process.

[diggnate]

QED

I'd love it if you wouldn't mind explaining the process by which this inventive machine operates.

[Goat]

Can you prove that statement 'the first ogranism must have had at least 500,000 base pairs'.

Unless you've got some inventive idea as to how an organism could spontaneously sequence MORE than half a million base pairs into functional DNA, then you have to assume the simplest organism was first. You could, I assume, claim that the organism had less than half a million BPs, but that would further prove my point.

I recommend reading up on any reputable abiogenesis research. They make the claims, not me. Unless of course, you think that the first organism contained 2.3+ billion base pairs too, and just degeneratively evolved over the last 3 billion years. Of course, that would mean the "tree of life" is upside down, and would also answer my question about evolution being a progressive process.

I want you to back up your statement 'the first organism must have at least 500,000 base pairs'. You then make a very nebiously statement saying basically,
'look it up yourself'.

That is the classic signs of avoidence. I don't think you have a source for your claim that is anything besides a faith based Christian 'I.D.' site, such as the discovery institute, or Dembski's claims.

You make the claim, you provide the reference.

[diggnate]

I want you to back up your statement 'the first organism must have at least 500,000 base pairs'. You then make a very nebiously [sic] statement saying basically,
'look it up yourself'.

That is the classic signs of avoidence. I don't think you have a source for your claim that is anything besides a faith based Christian 'I.D.' site, such as the discovery institute, or Dembski's claims.

You make the claim, you provide the reference.

First of all, this is all theoretical study, so asking me to "prove" a theoretical analysis is ridiculous. Second of all, ID research groups have just as much a right to write articles concerning genetics and biochemistry as anyone else does. They earned their degrees the same way the other guys did.

Thirdly, do you even understand the point of my statement? I'll give you a reference, but you need to understand what significance this has. EVEN IF my information is outdated, and it has been shown that there is another organism functioning on less than 500,000 BPs (or, as I'm fully aware, there is ongoing research studying things like RNA-world, self-replicating molecules, etc.), my point remains the same. Either 1 of 2 things happened:

1) the first organism (our common ancestor) had very little genes (or none at all), thus requiring the addition of staggering amounts of genetic information, or

2) the first organism had the most genes of any organism ever to live, and thus degeneratively DE-volved into what we see today (the old, remove information representation to gain complexity argument).

My point remains the same regardless of the discoveries in theoretical abiogenesis.

Get it?

reference 1:
http://www.talkorigins.org/faqs/abioprob/abioprob.html
This proves my point even more, although it is a good bit of speculation. If what TO is claiming is correct (there's no way to know), then in order to go from this to humans would require the addition of mind-blowing amounts of functional information.

We can argue about their dubious conclusions later.

reference 2:
http://www.ncbi.nlm.nih.gov/entrez/quer ... s=7569993
"The complete nucleotide sequence (580,070 base pairs) of the Mycoplasma genitalium genome, the smallest known genome of any free-living organism..."

So, you have a choice of anywhere between the hypothetical claims from TO or the real life example of the lowest number of base pairs known to be alive today. Any way you slice it, my point is still the same (see above)

[Furrowed Brow]

In my lost post to did not offer a reply to my point that your notion of information loss is meaningless. This is the nub of the issue I think. You seem to counter it by offering more examples, of what I think is flawed logic.

Information loss? That is relative to the analysis you are making. As already said. Every change, in some respect, or at some level, can be argued to entail information loss. Thus it is an empty notion.

I think the logic behind you math is a tad slippery to say the least.

Go back and read the documentation of the nylon bug. It DID LOSE FUNCTION. It lost metabolic efficiency, while losing 50% of its ability to break down other composites. That is NOT net information gain, and it certainly IS NOT a net gain in functionality.

Ok. How have you made the loss of unction analysis. 1) Loss of metabolic efficiency, 2) 50% reduction of ability to break down other composites, 3) gain of new function. That's two exisitng areas in which the bacteria can still function and one new area.

an "informationally positive" mutation would be one that added new function to an organism through the introduction of new features or the addition of function of pre-existing features (through the addition of novel genetic sequences, proteins, etc. but we're trying to avoid the nuts and bolts for the purposes of this conversation), all the while NOT removing function from other areas of the organism, which results in a NET INFORMATION GAIN.

In your original definition you say information positive is the gaining of a function without removing function. The bacteria has lost functional efficiency in some area but gained a new function. So you are really talking about functional efficiency.

IPM does not mean losing function to gain function. If I lose the ability to smell, but in it's place I can hear frequencies only dogs can hear, that is NOT an informationally positive mutation. I'm talking about NET INFORMATION GAIN.

The bacteria has not lost an ability, it has only seen a reduction. And what does a 50% reduction really mean. A 50% reduction in the ability of a dog’s smell is still pretty efficient smelling ability. How do you quantify loss and gain, and play off one against the other

Where is the objective criteria? This looks like creative accountancy to me.

Information loss has nothing to do with the environment. The possession of function is not dependent on the use of the function. The propagation of that function is indeed dependent on the use, but not the possession. Your speaking in very relative terms.

This is so wrong. Yes I am speaking in relative terms because information is relative.

Say you have a unique mutation to your white blood cells that cause you no harm or benefit. However there is one virus if it were exist that would be fatal to all humans except you. Your mutation gives you immunity. But that virus does not exist nor ever exists. Your mutation is informational empty without that virus. Its functionality is meaningless without that virus. However logically it is possible. but some possible function is informationally empty without a real environment interaction.

Say there is a parasite that feeds on only one kind of white blood cell. Your mutated kind. That function is again a relationship between cell and parasite. No parasite no relationship no function. Ok that function is negative to survival. But you are not talking about survival. It is still information. Still logically possible. Unless of course the limites of genetic information are the limits imposed by the environment.

Your response suggest some implicit teleological/platonic philosophical baggage lurking in you notion of “information”.

As for the lactose tolerance. I’m willing to learn. Enlighten me.

[QED]

QED

I'd love it if you wouldn't mind explaining the process by which this inventive machine operates.

The process is, as I have already mentioned above, a direct application of the logical principles identified in Darwinian evolution by natural selection. I'm pretty sure that you'll have come across it already as it's a broad and well-established field, but if you'll excuse me I'll pull some quotes out of wikipedia which sum it up well enough for our purposes here.

A genetic algorithm (or short GA) is a search technique used in computing to find true or approximate solutions to optimization and search problems. Genetic algorithms are categorized as global search heuristics. Genetic algorithms are a particular class of evolutionary algorithms that use techniques inspired by evolutionary biology such as inheritance, mutation, selection, and crossover (also called recombination).

Genetic algorithms are implemented as a computer simulation in which a population of abstract representations (called chromosomes or the genotype or the genome) of candidate solutions (called individuals, creatures, or phenotypes) to an optimization problem evolves toward better solutions. Traditionally, solutions are represented in binary as strings of 0s and 1s, but other encodings are also possible. The evolution usually starts from a population of randomly generated individuals and happens in generations. In each generation, the fitness of every individual in the population is evaluated, multiple individuals are stochastically selected from the current population (based on their fitness), and modified (recombined and possibly mutated) to form a new population. The new population is then used in the next iteration of the algorithm.

Genetic algorithms find application in computer science, engineering, economics, chemistry, physics, mathematics and other fields.

As you can see, the range of applications is very broad and gives rise to a variety of implementations. For example:

Genetic programming (GP) is a patented[1] automated methodology inspired by biological evolution to find computer programs that perform a user-defined task. Therefore it is a machine learning technique that uses an evolutionary algorithm to optimize a population of computer programs according to a fitness landscape determined by a program's ability to perform a given computational task. The first experiments with GP were reported by Stephen F. Smith (1980)[2] and Nichael L. Cramer (1985),[3] as described in the famous book Genetic Programming: On the Programming of Computers by Means of Natural Selection by John Koza (1992).

GP is very computationally intensive and so in the 1990s it was mainly used to solve relatively simple problems. But more recently, thanks to improvements in GP technology and to the exponential growth in CPU power, GP has started delivering a number of outstanding results. At the time of writing, nearly 40 human-competitive results have been gathered, in areas such as quantum computing, electronic design, game playing, sorting, searching and many more.[4] These results include the replication or infringement of several post-year-2000 inventions[citation needed], and the production of two patentable new inventions.

It's also important to mention Evolvable Hardware just to underscore the way in which Evolutionary Algorithms can lead to physical products:

Software configurable hardware, such as Programmable Logic Arrays, are on the market which accept a bit string instruction which is used to configure or “wire up” a hardware circuit to give it a desired architecture. This can be done an indefinite number of times. By treating the bit string instruction as a Genetic Algorithm “chromosome”, one has the means to evolve hardware.

The physical hardware needn't be so obviously software configurable as in wiki's example. Anything that can be assembled robotically can be physically evolved. NASA publicize the fact that they employ these techniques to Evolve optimised hardware for mission critical applications. You will find that this is in recognition of the fact that the Evolutionary Algorithms are capable of coming up with smarter designs than the engineers who designed the algorithms could come up with. What isn't publicized so much is the investment made by the military-industrial sector into these techniques. NASA are not alone in recognizing the fact that nature has a built-in method for the generation of clever design.

[Furrowed Brow]

Hi diggnate

I’m hoping you will be able to comment on the meaninglesssness of information loss. In the meantime it might be fun to see what an information loss analysis makes of Carsonella. Ruddii. Here are some links:

http://www.seedmagazine.com/news/2006/1 ... alking.php

http://www.newscientist.com/channel/lif ... -date.html

http://www.pnas.org/cgi/content/full/10 ... 919?ck=nck

I am quoting from the New Scientist 21 October 2006. p9

The mitochondria that provide our cells with energy and the chloroplasts in plant cells…were once free-living bacteria….Now two new species of bacteria that live in insects have been found in the process of transition from free-living organism to organelle. There genomes are the smallest ever sequenced.

And it seems C.ruddii has suffered deleterious mutation.

C.ruddii has lost many basic functions, including the ability to replicate independently:

But....

the host cell now takes care of that. The bacterium pays for its keep, however, supplying its sap-eating insect host with amino acids…

Ok so C.ruddii seems to have lost some info here….but hang on….its gained a home, and can still replicate, and gets to go places it would not go without being transported by an aphid. So is there loss of function, or not loss of function? Moreover the aphid gains an amino acid maker, gain in function or not? And is not a symbiotic relationship more complex, and ads another layer of information to how the aphid gets its amino acid fix?