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Author Topic:   Evolving New Information
Jazzns
Member (Idle past 1985 days)
Posts: 2657
From: A Better America
Joined: 07-23-2004


Message 436 of 458 (544325)
01-25-2010 1:04 PM
Reply to: Message 435 by cavediver
01-25-2010 12:30 PM


Re: Metric!
Yes you are right, I was a bit too harsh but only because I backed off of the definition I am trying to drive home which is a distance between two points. Really I was just plain using an incorrect analogy. I should have talked about a measuring tool by which the difference of information between two things is concerned.

My main point still stands though that I think this is a more effective line of argument against the whole "information" gambit. Show me exactly how you tell that one thing has more or less information than another thing, regardless of what "information" really is, and then we can BEGIN to have a discussion about if it is possible for it to increase or decrease.


If a nation expects to be ignorant and free, in a state of civilization, it expects what never was and never will be. --Thomas Jefferson
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cavediver
Member (Idle past 1717 days)
Posts: 4129
From: UK
Joined: 06-16-2005


Message 437 of 458 (544332)
01-25-2010 1:54 PM
Reply to: Message 436 by Jazzns
01-25-2010 1:04 PM


Re: Metric!
Yes, agree totally. And few seem to appreciate the over-whelming importance of context and environment in trying to understand what is meant by "specified" information. How much "specified" information is there in a five second burst of white noise? And how does your answer change when I reveal that it was identical to a previously recorded burst of white noise, only played backwards?
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Percy
Member
Posts: 18307
From: New Hampshire
Joined: 12-23-2000
Member Rating: 3.2


Message 438 of 458 (544357)
01-25-2010 3:36 PM
Reply to: Message 429 by LucyTheApe
01-25-2010 9:42 AM


Re: What is information?
LucyTheApe writes:

This conversation is pointless unless we both define what we mean by information.

My definition : "a coded message".

Now can I please have you definition?

First, let's be very clear about one thing: you don't know how to calculate the information content of a dataset. Independent of whether your definition of information, "a coded message," is correct, it doesn't provide you any method of quantifying information. This was effectively made clear by your recourse to compilers as information measurement tools, despite that they give variable answers for the same program file.

I use Shannon information to calculate the amount of information in a set of data. This requires defining the message set, because communication of information requires reproducing at point B a message that originated at point A.

If our message set is 0 and 1, a message set of size 2, then the amount of information that can be communicated in a single message is log22=1 bit

If our message set is the digits from 0 to 9, a message set of size 10, then the amount of information that can be communicated in a single message is log210=3.32 bits.

If our message set is the letters from A to Z plus space, a message set of size 27, then the amount of information that can be communicated in a single message is log227=4.75 bits.

The reason we don't use programming examples to explain information theory is because a programming language is so incredibly complex because the message set is context dependent. For example, ask yourself what is the message set for the first field of your program. Here's a partial list:

  • //
  • /*
  • public
  • private
  • import
  • ...

I don't know how many messages are possible for that first field, but let's assign it a value X. So the information communicated by the first field of a Java program is log2X bits.

Now ask yourself what is the message set for the second field of your program. Well, that depends upon what the first field was. If the first field began a comment then pretty much anything goes until the end of the comment field. If the first field was "public" or "private" then the message "class" might follow, and there are other possibilities. So the information communicated by the second field is a function of the first field, we can call it log2f(field1) bits. That's what I meant by context dependent.

The third field's message set will be a function of the first two fields, and the fourth field's message set will be a function of the first three fields, and so forth. You can see that this gets complicated very quickly.

This is why you were immediately challenged when you claimed you knew how much information was contained in your Java program. You had already demonstrated you knew very little about information theory, yet here you were claiming you could solve the very, very complex problem of calculating how much information was in a simple program. We knew it couldn't be true.

This is why I suggest we talk about examples where we can actually calculate the information content. The example from Message 1 fulfills this requirement. Here's a message set of size 3 that for the sake of discussion we can say represents the alleles for three different eye colors in a population:

  • GGAACG (green eyes)
  • GGAACA (blue eyes)
  • GGCACG (yellow eyes)

If one individual in our population receives a mutation, then our population now has four alleles for eye color:

  • GGAACG (green eyes)
  • GGAACA (blue eyes)
  • GGCACG (yellow eyes)
  • GGCACA (brown eyes)

The amount of information in our population for eye color has just increased from log23 = 1.585 bits to log24 = 2 bits, an increase of .415 bits. Mutations are one way of increasing the amount of information in the genome of a population.

--Percy


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Taq
Member
Posts: 7672
Joined: 03-06-2009
Member Rating: 3.0


Message 439 of 458 (544400)
01-25-2010 11:15 PM
Reply to: Message 426 by LucyTheApe
01-25-2010 8:30 AM


Re: What is information?
So the hypothesis should also explain the bizarre appearance of this egg-laying, venomous, duck-billed, beaver-tailed, otter-footed cute little mammal;

Sure. I bet you that the platypus jaw is completely mammalian and completely unlike an actual duck's bill. I bet you that the lower jaw is made up of a single dentary bone. I bet you that the jaw is even home to specialized mammalian cheek teeth. I even bet that the platypus has a multiple bone middle ear that is derived from reptilian jaw bones. Want to find out who is right?

As for egg-laying, the platypus lays reptile-like leathery eggs, kind of what one would expect due to the fact that mammals evolved from basal reptiles.

As for the tail, beavers are hardly the only species with a flat tail and such a small change in morphology is not that hard to evolve in separate lineages.

As for webbed toes, there are humans with webbed toes. It's a very common variation in a ton of mammalian species.

Test with the bar set really low.

Since when is a fish with legs a low bar? Are you saying that we should not see a fish with legs if tetrapods evolved from lobed finned fish?


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Dr Adequate
Member
Posts: 16085
Joined: 07-20-2006
Member Rating: 10.0


Message 440 of 458 (544406)
01-26-2010 2:27 AM
Reply to: Message 439 by Taq
01-25-2010 11:15 PM


Platypus Diversion
I bet you that the jaw is even home to specialized mammalian cheek teeth.

You might lose that one --- platypods have lost most of their teeth (some people will tell you that they're completely edentate, but as far as I can make out they're wrong).

As for the tail, beavers are hardly the only species with a flat tail and such a small change in morphology is not that hard to evolve in separate lineages.

You're right. This is in fact a classic example of superficial convergent evolution. If you look at the tail of the beaver, it has a standard set of spindly caudal vertebrae and the oar shape is provided by flesh. But if you look at the tail of the platypus, the oar shape is actually skeletal.

(LucyTheApe might like to notice the vast morphological difference between the "bill" of a DBP and the beak of a bird.)

See here for more information.

Now, back to the topic ...

Edited by Dr Adequate, : No reason given.


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LucyTheApe
Inactive Member


Message 441 of 458 (544416)
01-26-2010 6:02 AM
Reply to: Message 438 by Percy
01-25-2010 3:36 PM


Re: What is information?
Can't answer the question. I'm over it Percy, time to move on. I might check back when Vatican takes a fresh look at the whole stupid theory in a couple of months. Meanwhile I'll find something better to do with my drink'n time. Thanks to everyone here at the forum.


There no doubt exist natural laws, but once this fine reason of ours was corrupted, it corrupted everything.

blɛz paskal


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Taq
Member
Posts: 7672
Joined: 03-06-2009
Member Rating: 3.0


Message 442 of 458 (544461)
01-26-2010 3:26 PM
Reply to: Message 440 by Dr Adequate
01-26-2010 2:27 AM


Re: Platypus Diversion
You might lose that one --- platypods have lost most of their teeth (some people will tell you that they're completely edentate, but as far as I can make out they're wrong).

quote:
Scanning microscopy of platypus teeth
Anatomy and Embryology, Volume 174, Number 1 / April, 1986

Keith S. Lester1, 2 and Alan Boyde1, 2

(1) Westmead Hospital Dental Clinical School, Westmead, N.S.W., Australia
(2) Department of Anatomy and Embryology, University College London, London, United Kingdom

Accepted: 15 November 1985

Summary Anorganic unerupted developing teeth and airdired erupted teeth of the platypus (Ornithorhynchus anatinus) were examined in a scanning electron microscope and in a tandem scanning reflected light microscope. Typically mammalian developing fronts of enamel and dentine were identified in the anorganic unerupted specimens. The developing teeth were particularly small and fragile and the enamel elusive and difficult to examine in the normal way for morphological detail. Prepared fractured surfaces of unerupted specimens revealed preferentially oriented crystallite groups in the enamel generally perpendicular to the developing front and a highly globular, mineralized pattern in the dentine with fine diameter, sparsely distributed dentinal tubules.
Although optically homogeneous, the enamel of both developing and mature teeth displayed well-defined incremental lines, radial clefts, crystallite domains of variable size and outline, and fine tubules when examined by high contrast, back-scattered electron imaging. The enamel is prismatic only in part; well-formed, regular prisms not being a primary feature of platypus enamel. This can be related to the variability inherent in the developing surface and the thinness of the enamel layer. No surface was found which could be confidently identified as cementum; those developing surfaces not covered by enamel displaying small calcospherites which elsewhere marked the outer aspect of the dentine.



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barbara
Member (Idle past 2876 days)
Posts: 167
Joined: 07-19-2010


Message 443 of 458 (581007)
09-12-2010 10:13 PM
Reply to: Message 442 by Taq
01-26-2010 3:26 PM


Re:Viruses
The Genome Institute of Singapore states that a virus millions of years ago in humans is how embryonic stem cells get turned on and off. The viral transposable gene carrying binding sites for regulatory elements to new locations.

I had also heard some time ago that a virus was implicated is how mammals obtained the placenta.

Doesn't this seem odd to anyone that a virus can do this? How come flu viruses only make us sick?

Edited by barbara, : No reason given.


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Wounded King
Member (Idle past 2168 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 444 of 458 (581028)
09-13-2010 2:52 AM
Reply to: Message 443 by barbara
09-12-2010 10:13 PM


Re: Re:Viruses
Doesn't this seem odd to anyone that a virus can do this?

I'm not sure why it should particularly, can you explain?

How come flu viruses only make us sick?

Because influenza isn't a retrovirus with the capacity to insert itself into a genome.

TTFN,

WK


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Nij
Member (Idle past 2963 days)
Posts: 239
From: New Zealand
Joined: 08-20-2010


Message 445 of 458 (581041)
09-13-2010 6:18 AM
Reply to: Message 443 by barbara
09-12-2010 10:13 PM


Re: Re:Viruses
Doesn't this seem odd to anyone that a virus can do this?

If by "odd" you mean "not what was expected" then yeah, lots of people. That's why they study them and the result is knowledge of things called retroviruses as WK mentioned. Incidentally, that knowledge is vital to things like finding a treatment for HIV, which is a retrovirus.

Influenza is not one. Otherwise we would have one hell of a larger problem than simply worrying about seasonal 'flu': retroviruses are not the easiest thing to treat, as the prevalence of AIDS has demonstrated, because of the very nature of the virus (being protected by basically "hiding"in our own DNA).


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barbara
Member (Idle past 2876 days)
Posts: 167
Joined: 07-19-2010


Message 446 of 458 (581055)
09-13-2010 9:24 AM
Reply to: Message 445 by Nij
09-13-2010 6:18 AM


Re: Re:Viruses
I had read about ERV's but didn't realize fully how directly involved they are in turning switches on and off, moving genes around that function without killing the host. Control the timing of growth patterns. We really are a living machine that evolved by non living entities that enter us and become living (they look like space probes) with specific targets to reconstruct the hardware with updated software.

Does science know yet how retroviruses are formed?


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Wounded King
Member (Idle past 2168 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 447 of 458 (581065)
09-13-2010 10:48 AM
Reply to: Message 446 by barbara
09-13-2010 9:24 AM


Re: Re:Viruses
Does science know yet how retroviruses are formed?

I assume you mean do we know where retroviruses came from originally. In terms of how new retroviral vectors are formed during viral replication we have a pretty extensive understanding.

The short answer is not exactly, but most current genetic research points to retroviruses being derived from transposable elements native to organismal genomes called Long Terminal Repeat (LTR) retrotransposons.

TTFN,

WK


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Dr Jack
Member (Idle past 178 days)
Posts: 3507
From: Leicester, England
Joined: 07-14-2003


Message 448 of 458 (581088)
09-13-2010 2:34 PM
Reply to: Message 447 by Wounded King
09-13-2010 10:48 AM


Re: Re:Viruses
The short answer is not exactly, but most current genetic research points to retroviruses being derived from transposable elements native to organismal genomes called Long Terminal Repeat (LTR) retrotransposons.

Really? Interesting. I was under the impression the generally held view was that retroviruses pre-dated the domain split, since certain retroviral proteins from different domains of life are most closely related to each other than they are to any host protein. I was also under the impression that transposons were thought most likely to be degenerate viruses whose evolutionary pathway had taken them away from having a separate infective stage.

Do you have sources I can look at?


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Taq
Member
Posts: 7672
Joined: 03-06-2009
Member Rating: 3.0


Message 449 of 458 (581100)
09-13-2010 5:08 PM
Reply to: Message 446 by barbara
09-13-2010 9:24 AM


Re: Re:Viruses
I had read about ERV's but didn't realize fully how directly involved they are in turning switches on and off, moving genes around that function without killing the host.

You must also remember that this is exactly what the viral genes evolved for. Bookending the viral genomes are the long tandem repeats which serve as strong promoters for the viral genes that sit between them. This is how the virus hijacks the host transcription machinery to produce more virus. Then you also have the viral reverse trascriptase gene which makes DNA copies from the viral RNA. You also have viral integrase genes that are involved in inserting the viral genome into the host DNA. There are also viral envelope genes that are involved in making viral particles that are capable of binding to other cells (which may explain why these genes are important in placental development).

So we can see that the roles these genes evolve into within the host genome are very similar to their original roles as part of viral replication and infection.


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Wounded King
Member (Idle past 2168 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 450 of 458 (581116)
09-13-2010 7:34 PM
Reply to: Message 448 by Dr Jack
09-13-2010 2:34 PM


Re:Viruses
I was also under the impression that transposons were thought most likely to be degenerate viruses whose evolutionary pathway that has taken them away from having a separate infective stage.

This may still be the case in many cases as there is clearly a complex dynamic between LTR transposable elements and retroviruses. It is also possible that there is a viral, but not retroviral, origin for such elements.

Phylogenies of ribonuclease H (RNH) suggest that LTRs and retroviruses arose quite late in eukaryotes possibly derived from a fusion of DNA mediated transposon and non-LTR retrotransposon (Malik and Eickbush, 2001; Malik, 2005).

There is also evidence suggesting that in some cases env genes conferring infectivity have been co-opted from non-retroviral viruses (Malik et al., 2000; Havecker et al., 2004; Eickbush and Jamburuthugoda, 2008).

TTFN,

WK


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