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Discussing the gaps in evolution theory

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posted on Jul, 17 2016 @ 12:54 PM
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a reply to: burgerbuddy

Who says it isn't?




posted on Jul, 20 2016 @ 06:05 PM
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a reply to: ChaoticOrder

Yes indeed there are holes in the theory of evolution. That is how science often happens, but those holes get filled (and they have been) and other bits get rewritten with new evidence.

With the advent of genetic sequencing, and computers capable of crunching whole genomic data. Many mysteries have been opened wide.

To counter your comments. How complete (I mean evidence) are the competing theories to evolution?



posted on Jul, 21 2016 @ 01:06 AM
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a reply to: ChaoticOrder

I am a software developer as well so if this is really your goal, then you need to take a few classes in biochemistry and genetics. From my research macro-evolution simply cannot occur in reality. However, as the intelligent mind behind the process you could rig it to work correctly by filling in the holes. For example, for new species to form you cannot simply mutate DNA indefinitely. You need to work in something similar to the concept of epigenetics.

ghr.nlm.nih.gov...

"DNA modifications that do not change the DNA sequence can affect gene activity. Chemical compounds that are added to single genes can regulate their activity; these modifications are known as epigenetic changes. The epigenome comprises all of the chemical compounds that have been added to the entirety of one’s DNA (genome) as a way to regulate the activity (expression) of all the genes within the genome. The chemical compounds of the epigenome are not part of the DNA sequence, but are on or attached to DNA (“epi-“ means above in Greek). Epigenomic modifications remain as cells divide and in some cases can be inherited through the generations. Environmental influences, such as a person’s diet and exposure to pollutants, can also impact the epigenome.

Epigenetic changes can help determine whether genes are turned on or off and can influence the production of proteins in certain cells, ensuring that only necessary proteins are produced. For example, proteins that promote bone growth are not produced in muscle cells. Patterns of epigenome modification vary among individuals, different tissues within an individual, and even different cells.

A common type of epigenomic modification is called methylation. Methylation involves attaching small molecules called methyl groups, each consisting of one carbon atom and three hydrogen atoms, to segments of DNA. When methyl groups are added to a particular gene, that gene is turned off or silenced, and no protein is produced from that gene.

Because errors in the epigenetic process, such as modifying the wrong gene or failing to add a compound to a gene, can lead to abnormal gene activity or inactivity, they can cause genetic disorders. Conditions including cancers, metabolic disorders, and degenerative disorders have all been found to be related to epigenetic errors."


The problem is in reality these can only be passed on in the germline. Leave that out of your program and make it better. Any epimutation can be passed on to the child, and use the epigenome to help the program determine what "genes" need to be used and what genes don't. Next build epimutators. Epimutations would need to involve a base class for tagging machines and then somehow build new or adapt old tagging machines, but they need to know where in all the genome to place the tags to help determine whether this gene is expressed or not expresse. Likewise for the machines that remove and move the tags. In other words, it is not good enough merely to evolve the machines. They somehow much know where to place the tags given a spectrum of environmental signals.And then the machines that interpret the tags would have to do so correctly. They would have to know what the tag means. So again, not only must these machines have evolved or adapted, but they must know what they are doing. Honestly don't think its possible to replicate this in code, life is simply to complex but it is a fun problem to think about.


Then you also need to work in a concept of embryonic development. The issue in reality is that any changes to the developmental gene regulatory network cause catastrophic effects to the organism. You can look at fruit fly experiments to verify this, or dog breeders your choice. So again leave this out of the program. However with us being the Maker, we can do as we please. Early stage embryonic development in the program should have a high success rate and make major evolutionary changes again why not make it work because evolution definitely doesn't. Again don't think anyone can replicate this in code but have fun trying



posted on Jul, 21 2016 @ 02:50 PM
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a reply to: ServantOfTheLamb

Strange in another thread you claim not to understand the science involved. So is this research just watching videos online? OR are you actually taking papers in Chemistry, Biochemistry, Genetics, and bioiformatics? If you are a software developer, how is your R? You can go manipulate some data, for free, if you can code R well.



posted on Jul, 21 2016 @ 03:24 PM
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originally posted by: Noinden
a reply to: ServantOfTheLamb

Strange in another thread you claim not to understand the science involved. So is this research just watching videos online? OR are you actually taking papers in Chemistry, Biochemistry, Genetics, and bioiformatics? If you are a software developer, how is your R? You can go manipulate some data, for free, if you can code R well.


he quoted part of the article, then switched to a coding metaphor for the rest of it. information theory and evolution?


In biology the term information is used with two very different meanings. The first is in reference to the fact that the sequence of bases in DNA codes for the sequence of amino acids in proteins. In this restricted sense, DNA contains information, namely about the primary structure of proteins. The second use of the term information is an extrapolation: it signifies the belief or expectation that the genome somehow also codes for the higher or more complex properties of living things. It is clear that the second type of information, if it exists, must be very different from the simple one-to-one cryptography of the genetic code. This extrapolation is based, loosely, on information theory. But to apply information theory in a proper and useful way it is necessary to identify the manner in which information is to be measured (the units in which it is to be expressed in both sender and receiver, and the total amount of information in the system and in a message), and it is necessary to identify the sender, the receiver and the information channel (or means by which information is transmitted). As it is, there exists no generally accepted method for measuring the amount of information in a biological system, nor even agreement of what the units of information are (atoms, molecules, cells?) and how to encode information about their number, their diversity, and their arrangement in space and time


the point here is not to debunk evolution, but to shed some light on its fuzzy areas. so sayeth the op, as foretold by the scrolls.



The long-running puzzlement about the appearance of the Cambrian fauna, seemingly abruptly, without precursor, centers on three key points: whether there really was a mass diversification of complex organisms over a relatively short period of time during the early Cambrian; what might have caused such rapid change; and what it would imply about the origin of animal life.


rapid? this took at least 5 million years. and a fraction of that period was successfully fossilized. and a fraction of said fossils have been successfully collected. the investigation is on going, but it has given us a pretty good picture already. no "implying" necessary.

edit on 21-7-2016 by TzarChasm because: (no reason given)



posted on Jul, 21 2016 @ 03:42 PM
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a reply to: TzarChasm

To be fair discussions on anything genetic are hampered by the idea that DNA (and by extension RNA) are data. Rather than chemical potential
Its understandable to the uninitiated, given that the term codon (via code) still exists. But data is a poor analogy. Oh wait this discussion has happened recently with that poster



posted on Jul, 21 2016 @ 03:44 PM
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a reply to: TzarChasm

Now as to debunking evolution? I've already asked, what about the alternatives, or are we just picking on evolution because faith says too? Which version of evolution? Darwins? The current one? OR the good old "information theory because they use evolution as a term there too" one?



posted on Jul, 21 2016 @ 03:53 PM
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originally posted by: Noinden
a reply to: TzarChasm

Now as to debunking evolution? I've already asked, what about the alternatives, or are we just picking on evolution because faith says too? Which version of evolution? Darwins? The current one? OR the good old "information theory because they use evolution as a term there too" one?


i wasnt aware that there is a viable alternative to modern evolutionary synthesis. MES is the most accurate and reliable model available, i dont know why anyone would want to downgrade. darwins model of evolution became the basis for todays model although there have been, how would you say, amendments. i have already shared the relevant selection on the relationship between information theory and evolution.



posted on Jul, 21 2016 @ 03:56 PM
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a reply to: TzarChasm

Oh did I say viable? I thought it would be fair that all alternatives be examined, and deconstructed, and the one with the fewest number of gaps, wins? Sound reasonable ?



posted on Jul, 21 2016 @ 04:00 PM
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originally posted by: Noinden
a reply to: TzarChasm

Oh did I say viable? I thought it would be fair that all alternatives be examined, and deconstructed, and the one with the fewest number of gaps, wins? Sound reasonable ?


we already know which one has the fewest gaps.



posted on Jul, 21 2016 @ 04:01 PM
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a reply to: TzarChasm

You and I do, but we most likely understood the science involved, rather than cut and pasting from various creationist sites.



posted on Jul, 21 2016 @ 05:11 PM
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originally posted by: ServantOfTheLamb
a reply to: ChaoticOrder

I am a software developer as well so if this is really your goal, then you need to take a few classes in biochemistry and genetics.

Well, you actually said something that made sense; however, you followed with your usual nonsense and misrepresentations.



posted on Jul, 22 2016 @ 10:16 AM
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a reply to: ServantOfTheLamb


I am a software developer as well so if this is really your goal, then you need to take a few classes in biochemistry and genetics.

If you mean watch lectures on YouTube I'm way ahead of you lol. One lecture series I found particularly insightful was a molecular genetics series from Standford. Robert Sapolsky does a really nice job covering topics such as transposable genes and epigenetics, and things we've discussed in this thread, such as gene duplication as a form of redundancy.





Again don't think anyone can replicate this in code but have fun trying

My goal isn't really to simulate the exact way real life organisms evolve or how they develop, that would be more of a bioinformatics problems. Like you said, there may be shortcuts and optimizations that can be made which don't happen in real life. What I want to do is take concepts from biology and interpret them using ideas from computer science and information theory so I can strip them down to their essence. For example our genes aren't just laid out in neat discrete little packets, they are broken up and dispersed throughout the genome, evolution is a very messy process and doesn't care about producing elegant well organized code. The idea of dispersed modular genes relates to concepts of modular function libraries and sub-routines. In other words, many complex mechanisms are built from many simpler building blocks, and the padding between the blocks is instructions for how to put them together, when to use them, how to use them, etc. The same sort of interpretations can be applied to things like gene duplication and transposition, they provide things such as code redundancy and dynamic adaptation.
edit on 22/7/2016 by ChaoticOrder because: (no reason given)



posted on Jul, 22 2016 @ 10:27 AM
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a reply to: Noinden


To be fair discussions on anything genetic are hampered by the idea that DNA (and by extension RNA) are data.

At the end of the day everything is data. Just because we don't know exactly how to measure the amount of information in the human genome doesn't mean it cannot be done. We use magnetically aligned molecules to store information on a hard disk drive, however evolution has clearly found a much more efficient way to store information using molecules. There is a finite limit to how small our HDD's can get because there is a limit to how much information particles can hold, there's a bit limit and our DNA encoding is probably near that limit. And even if you can measure the exact number of bits in our genome that's still quite a deceptive measure of information because as I said in my last post, DNA sequences can be put together in a modular fashion to create a huge amount of variety and much more complexity than you would guess just by looking at the size of the genome, much like a procedural game can be small in size but contain a huge amount of procedurally generated content.



posted on Jul, 22 2016 @ 08:41 PM
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originally posted by: ChaoticOrder
a reply to: Noinden


To be fair discussions on anything genetic are hampered by the idea that DNA (and by extension RNA) are data.

At the end of the day everything is data. Just because we don't know exactly how to measure the amount of information in the human genome doesn't mean it cannot be done. We use magnetically aligned molecules to store information on a hard disk drive, however evolution has clearly found a much more efficient way to store information using molecules. There is a finite limit to how small our HDD's can get because there is a limit to how much information particles can hold, there's a bit limit and our DNA encoding is probably near that limit. And even if you can measure the exact number of bits in our genome that's still quite a deceptive measure of information because as I said in my last post, DNA sequences can be put together in a modular fashion to create a huge amount of variety and much more complexity than you would guess just by looking at the size of the genome, much like a procedural game can be small in size but contain a huge amount of procedurally generated content.


still not sure what this has to do with gaps in evolution.



posted on Jul, 24 2016 @ 07:57 PM
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a reply to: ChaoticOrder

This has what to do with this discussion? No seriously, just because some researchers have the potential to use DNA to store digital data, does not mean that our genomes are, digital data.

If you really want to make this sort of flawed analogy, DNA is not a doccument made of data, it is the application which allows you to access the data.



posted on Jul, 25 2016 @ 04:48 AM
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a reply to: ChaoticOrder


What I want to do is take concepts from biology and interpret them using ideas from computer science and information theory so I can strip them down to their essence.


The problem with this is that biology and computer science are completely separate unrelated concepts. Information theory applies to computer software only. It's like taking concepts from geology and using ideas from NFL football to have a deeper understanding of it. It really just muddies the waters. If somebody could prove DNA was digital, it would be a different story, but you seem to be interpreting it metaphorically.



posted on Jul, 25 2016 @ 08:24 PM
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a reply to: Barcs


The problem with this is that biology and computer science are completely separate unrelated concepts.

Actually no they're not, they are indeed very closely related topics. Humans are biological machines regardless of whether you want to believe that or not. We aren't some mystical entities that walk around due to magic, no the neural networks in our brains are performing computations to help us survive in the world we live in. We are able to walk because our brain sends signals to our muscles causing them to contract at the right time. Computational biology is an entire field dedicated to creating algorithms based on how biological systems solve problems, so to say the two topics are completely unrelated is extremely naive.

The way I see it, living systems are self-replicating biological machines, and the processes they use to replicate can be emulated by computers. What's really interesting, is that when you actually look at how reproduction works in living organisms it actually does have many strong connections to information theory, especially when it comes to topics such as error correction. Quantum mechanics tells us that all energy states are quantized, there is no such thing as fractional or infinite energy states in nature, so in reality EVERYTHING can be distilled down to digital information, which is why some scientists believe we could be living in a computer simulation.
edit on 25/7/2016 by ChaoticOrder because: (no reason given)



posted on Jul, 25 2016 @ 08:31 PM
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a reply to: ChaoticOrder

Demonstrate that they are closely related. Saying that it is, and the fact that it is are two different things. I've degrees in Chemistry, Biochemistry and Bioinformatics, the last one if you don't know is a hybrid of Biochem/Genetics with COmp Sci, and Statistics. I'll say again, they are not that closely related.



posted on Jul, 25 2016 @ 09:25 PM
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originally posted by: ChaoticOrder
a reply to: Barcs


The problem with this is that biology and computer science are completely separate unrelated concepts.

Actually no they're not, they are indeed very closely related topics. Humans are biological machines regardless of whether you want to believe that or not. We aren't some mystical entities that walk around due to magic, no the neural networks in our brains are performing computations to help us survive in the world we live in. We are able to walk because our brain sends signals to our muscles causing them to contract at the right time. Computational biology is an entire field dedicated to creating algorithms based on how biological systems solve problems, so to say the two topics are completely unrelated is extremely naive.

The way I see it, living systems are self-replicating biological machines, and the processes they use to replicate can be emulated by computers. What's really interesting, is that when you actually look at how reproduction works in living organisms it actually does have many strong connections to information theory, especially when it comes to topics such as error correction. Quantum mechanics tells us that all energy states are quantized, there is no such thing as fractional or infinite energy states in nature, so in reality EVERYTHING can be distilled down to digital information, which is why some scientists believe we could be living in a computer simulation.


Actually, you are correct. Code is code. It comes down to a question of translation, interpretation and confluence. The article below describes how DNA can store digital information. Binary code to a 4 letter code - a big leap technologically, but not a big leap when you realize that codes can be broken and reprogrammed into an entirely different language. Right now it's storage. But translating the DNA code into other languages isn't far off.


Scientists Work Toward Storing Digital Information in DNA

"Into this world comes the notion of DNA storage. DNA is by its essence an information-storing molecule; the genes we pass from generation to generation transmit the blueprints for creating the human body. That information is stored in strings of what's often called the four-letter DNA code. That really refers to sequences of four building blocks -- abbreviated as A, C, T and G -- found in the DNA molecule. Specific sequences give the body directions for creating particular proteins.

Digital devices, on the other hand, store information in a two-letter code that produces strings of ones and zeroes. A capital "A," for example, is 01000001."
edit on 25-7-2016 by Phantom423 because: (no reason given)


www.sci-tech-today.com...
edit on 25-7-2016 by Phantom423 because: (no reason given)



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