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originally posted by: peter vlar
When you climb a mountain to an altitude where the air is thinner and slowly acclimate to it is not adaptation.
originally posted by: Noinden
a reply to: cooperton
NO try again: In biology, an adaptation, also called an adaptive trait, is a trait with a current functional role in the life of an organism that is maintained and evolved by means of natural selection. (1)
(1) Huxley, Julian (1942). Evolution: The Modern Synthesis. p. 449
The reason DNA is NOT information in the sense of information theory, is there is no predetermined outcome (like say a book, or a program). So yeah it's information of a sort, but far more than that, what alphabet, or language do you know that self replicates, all on it's lonesome?
Could I say then that you have a bias toward more of a chemical view of DNA. But you are also in bioinformatics, right? Doesn't that involve the analysis of raw biological data?
I have no idea how you would argue that this is not adaptation.
originally posted by: rnaa
a reply to: cooperton
I have no idea how you would argue that this is not adaptation.
Because you are using the word 'adaptation' in a general usage form.
Biology has a very specific use of the word.
You are discussing biology, so you need to understand and use the words as they are used in biology.
Your body is 'acclimating' not 'adapting'. When you leave the high mountains, your body will re-acclimatize to the lower altitude.
Individuals acclimatize, populations adapt.
originally posted by: cooperton
originally posted by: rnaa
a reply to: cooperton
I have no idea how you would argue that this is not adaptation.
Because you are using the word 'adaptation' in a general usage form.
Biology has a very specific use of the word.
You are discussing biology, so you need to understand and use the words as they are used in biology.
Your body is 'acclimating' not 'adapting'. When you leave the high mountains, your body will re-acclimatize to the lower altitude.
Individuals acclimatize, populations adapt.
Swimming in semantic soup. I'm not excluding myself when I say Everyone does it when discussing the theory of evolution. It's like trying to eat soup with a fork - sure you're bound to get some chunks out of there, but most of it remains irretrievable.
Adaptation: "a change or the process of change by which an organism or species becomes better suited to its environment."
The book Information Theory, Evolution and the Origin of Life is written by Hubert Yockey, the foremost living specialist in bioinformatics. The publisher is Cambridge University press. Yockey rigorously demonstrates that the coding process in DNA is identical to the coding process and mathematical definitions used in Electrical Engineering. This is not subjective, it is not debatable or even controversial. It is a brute fact:
“Information, transcription, translation, code, redundancy, synonymous, messenger, editing, and proofreading are all appropriate terms in biology. They take their meaning from information theory (Shannon, 1948) and are not synonyms, metaphors, or analogies.” (Hubert P. Yockey, Information Theory, Evolution, and the Origin of Life, Cambridge University Press, 2005)
All the information needed to make a living, self-replicating cell is locked up within the spirals of DNA's double helix. As we read and interpret that software of life, we should be able to completely understand how cells work, then change and improve them by writing new cellular software.
The software defines the manufacture of proteins that can be viewed as its hardware, the robots and chemical machines that run a cell. The software is vital because the cell's hardware wears out. Cells will die in minutes to days if they lack their genetic-information system. They will not evolve, they will not replicate, and they will not live.
This week, Microsoft has announced a partnership that could fundamentally transform our relationship with our past and the future.
Twist Bioscience has handed Microsoft 10 million long oligonucleotides of DNA molecules (quite a lot), so it can start testing the use of this “prehistoric information technology” for long-term, secure data storage.
Like computers, DNA molecules encode information into discrete units. DNA is made up of four of these, called nucelotides and referred to as A, C, G and T, rather than zeroes and ones. Long strands of DNA are made up of a sequence of these, with a particular order representing a specific piece of information.
originally posted by: cooperton
If a genetic code and the information encoded in such does not suffice for you to indicate a coder, what could possibly demonstrate to you that there was an intelligent designer that designed this intelligent code?
originally posted by: whereislogic
originally posted by: TREESNAKE1111
The argument is about bio-Genesis , not evolution per-se . Without data dna is just a string of molecules stuck together incapable of doing anything .
... certain people try to seperate the subject of what they refer to as "evolution" from "abiogenesis" but when a thread like this pops up the arguments against some of the conclusions involving the word "design", "designer", etc. are remarkably similar to those arguing in favor of what they sometimes refer to as "biological evolution"...
In essence:
'nature did it'
...
Perhaps it has something to do with the famous and prominent evolutionary philosophers Haldane and Oparin referring to what Huxley referred to as "the hypothesis of abiogenesis" as "the chemical evolution theory of life". Which is one of the many fancy ways of saying:
'Mother Nature did it' ('Gaia did it')
originally posted by: Noinden
It is chemical potential. The problem with analogies (and Watson and Crick forced this analogy by using the word "code" (still used in "codon")) is they are not very good beyond the basic level.
originally posted by: Noinden
The reason DNA is NOT information in the sense of information theory, is there is no predetermined outcome (like say a book, or a program). So yeah it's information of a sort, but far more than that, what alphabet, or language do you know that self replicates, all on it's lonesome?
Good point. Few have realized or meditated on this concept.
If an opportunity for a beneficial mutation only occurs once every generation,
One kind of rate is the error rate of DNA replication. This is close to 1.0 × 10-8 for replication complexes that are capable of proofreading. Many errors are repaired by repair enzymes and this process is about 99% efficient. Thus, the overall error rate is close to 1.0 × 10-10 per bp.
Given that the human genome is 3.2 × 109 bp, this means that there are on average 0.32 new substitutions every time the complete genome is replicated. In humans there are about 30 cell generations between zygote and egg cells and about 400 cell divisions between zygote and mature sperm. Thus, in males, the sperm cells have about 128 new mutations and the haploid egg genome has about 10 new mutations for a total of 138 new mutations in every new zygote. Let's round this down to 130 mutations per generation.1 I call this the "biochemical method" of calculating mutation rate
The second method is something I call the "phylogenetic method" [Estimating the Human Mutation Rate: Phylogenetic Method]. It's based on the idea that the vast majority of mutations in primate genomes are in junk DNA. That means they are neutral. If we compare the genomes of different primate species, we can calculate a mutation rate based on population genetics, which postulates that the rate of fixation of neutral alleles is the same as the mutation rate.
This gives mutation rates of 112-160 mutations per generation. That value depends on knowing the time of divergence of different lineages (e.g. humans and chimpanzees) and the generation times. Both of these values are subject to uncertainty but they can't be off by very much. Certainly not by a factor of two or more.
The third method is the "direct method" [Estimating the Human Mutation Rate: Direct Method]. This is where you sequence the genomes of parents and their offspring or you sequence the genomes of two individuals who descend from a common ancestor. All you need to do is count the number of new mutations and you get the mutation rate directly.
These experiments yield a range of values from a low of 56 mutations per generation to a high of 103 mutations per generation. Most of the values cluster around 75 mutations per generation and that's what gives rise to the controversy. The direct method gives mutation rates the are about half the rate of other methods.
The direct method is not very reliable since the quality of the genome sequences is low and only a faction of the genomes is actually sequenced. Typically about 60-80% of the genome sequence is reliable. The number of potential sequencing errors overwhelms the number of possible mutations so a lot of "adjusting" is necessary in order to weed out false positives and false negatives. Nevertheless, it's satisfying that the results are in the right ballpark.
A slower molecular clock worked well to harmonize genetic and archaeological estimates for dates of key events in human evolution, such as migrations out of Africa and around the rest of the world. But calculations using the slow clock gave nonsensical results when extended further back in time — positing, for example, that the most recent common ancestor of apes and monkeys could have encountered dinosaurs.
With approximately 3,200,000,000 nucleotides in the human genome,
it seems unfathomable that even 1,000,000,000 years could have allowed so many beneficial mutations to occur -
especially when no known beneficial mutation has graced humanity in our written history.
C-C chemokine receptor type 5, also known as CCR5 or CD195, is a protein on the surface of white blood cells that is involved in the immune system as it acts as a receptor for chemokines. This is the process by which T cells are attracted to specific tissue and organ targets. Many forms of HIV, the virus that causes AIDS, initially use CCR5 to enter and infect host cells. Certain individuals carry a mutation known as CCR5-Δ32 in the CCR5 gene, protecting them against these strains of HIV.
In humans, the CCR5 gene that encodes the CCR5 protein is located on the short (p) arm at position 21 on chromosome 3. Certain populations have inherited the Delta 32 mutation resulting in the genetic deletion of a portion of the CCR5 gene. Homozygous carriers of this mutation are resistant to M-tropic strains of HIV-1 infection.
...
The CCR5 Δ32 allele is notable for its recent origin, unexpectedly high frequency, and distinct geographic distribution,[30] which together suggest that (a) it arose from a single mutation, and (b) it was historically subject to positive selection.
Two studies have used linkage analysis to estimate the age of the CCR5 Δ32 deletion, assuming that the amount of recombination and mutation observed on genomic regions surrounding the CCR5 Δ32 deletion would be proportional to the age of the deletion.[23][31] Using a sample of 4000 individuals from 38 ethnic populations, Stephens et al. estimated that the CCR5-Δ32 deletion occurred 700 years ago (275-1875, 95% confidence interval). Another group, Libert et al. (1998), estimated the age of the CCR5 Δ32 mutation is based on the microsatellite mutations to be 2100 years (700-4800, 95% confidence interval).
originally posted by: rnaa
What other view is there? DNA is made up of chemicals. Those chemicals obey the 'laws' of physics.
Codons are biological data, meaning they are a base for a chemical reaction to take place. They are not information and cannot be identified with data or information in computer science. As I said above even calling them data is a stretched metaphor.
A gene is a set of related codons which could be compared to a dataset in our stretched analogy. It is not information either.
A DNA strand is a set of of genes which could be compared to a database containing many datasets. It is not information either.
originally posted by: rnaa
There are actually 6.4 billion base pairs (64,000,000,000) in the human genome.
The human genome contains approximately 3 billion of these base pairs, which reside in the 23 pairs of chromosomes within the nucleus of all our cells. Each chromosome contains hundreds to thousands of genes, which carry the instructions for making proteins. Each of the estimated 30,000 genes in the human genome makes an average of three proteins.
Given that the human genome is 3.2 × 109 bp, this means that there are on average 0.32 new substitutions every time the complete genome is replicated.
Given that the human genome is 3.2 × 10**9 bp, this means that there are on average 0.32 new substitutions every time the complete genome is replicated.
The human genome consists of 6.4 × 10**9 base pairs (6.4 billion). That works out to 6.4 mutations per year.
Can you define what a gene is.
You explained to me how sexual reproduction works? In what universe?
I'm asking you to define a gene because I want to see what you're going to say it is.