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Author
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Topic: From Chimpanzee genome to human genome
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Zia H. Shah
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Member # 284
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posted 29. May 2002 08:58
From Chimpanzee genome to human genome
It is said that chimpanzee genome is 98% same as that of the human genome. We will take it on face value. It creates a superficial impression that it is easy to get the other 2%. It is easy to understand that writing of 2% of Encyclopedia Britannica by a chimpanzee jumping up and down the keyboard of a word processor will not accomplish the job. Even creating one line of English text at random has huge odds.
Richard Dawkin in his book The blind watchmaker has described a good analogy. The analogy is right and correct even though the application is wrong. He describes it in the chapter “accumulating small change”. It basically says that if we want to create a sentence from Shakespeare
Methinks it is like a weasel
by completely random process then the odds of getting one are about 1 in 10,000 million million million million million million. However, if there were some artificial or real intelligence, that freezes the success, every time the correct alphabet accidentally hits one of the 27 spots, or every time there is movement in the right direction, then the job can be accomplished in 40-50 generations. So, far it is narration of statistical facts, however, the application of the analogy by Dawkins is wrong. He assumes that mutations can serve as the randomness to move the letters around and natural selection will do the job of fixing the alphabets in proper position. Here, he is wrong. The natural selection does not have intelligence!
Let me present as food for thought, what I believe to be, a better utilization of this analogy.
There are proof-reading mechanisms in the genome that ensure the accuracy of the replication of DNA. In other words, the genome possesses some artificial intelligence. I personally do not know the full known details of such mechanisms, and am hoping that some one will enlighten us about those details in discussing this thread.
At any rate, if along side simple proof-reading mechanisms, a real intelligence has included additional artificial intelligence in the chimpanzee genome or earlier genomes, to select out any mutations that may be supportive of intellect or language capabilities as seen in humans then the job will be done.
The three million years from chimpanzees to humans is not enough time for natural selection to accomplish a whole lot. But if there are active mechanisms in the genome itself of selection then the job is doable.
It would be important for our organization to support research projects on finding additional functions in the so-called “Junk DNA”. There in may lie the ultimate answers. Discovering, selection mechanisms (artificial intelligence) in the DNA will move our debate with the Darwinians from theoretical to pragmatic grounds and will serve the cause of science and research at the same time. If we find such artificial intelligence in genomes then our debate will shift to how some real intelligence put such artificial intelligence in the system.
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warren_bergerson
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Member # 262
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posted 29. May 2002 09:39
The evolution from apes or man, or the ‘evolution of humanness’ is as you suggest a very interesting and important subject for analysis. I think, however, you will miss the significance of this evolutionary event if you start with the assumption that the evolutionary change is explained by ‘the 2% change in DNA’. I would suggest that the analysis will be much more productive if you start with the equally reasonable assumptions that:
1. The evolution of humanness represents the evolution of a new evolutionary process.
2. The evolution of humanness is largely independent of genetic change.
Starting with these assumptions we can construct a number of hypothesis that clearly seem to fit the known data including:
1. Humanness, or the evolution of humanness, is associated with a dramatic increase in creative intelligence or with a dramatic increase in the ability to produce creative results.
2. The increase in creative intelligence did not occur evenly over the last 3 million years, but at ever increasing rates as observed over the last 100,000, 10,000, 1,000, or 100 years.
3. Human creative intelligence continues to evolve rapidly.
Traditional analysis of the evolution of humanness starts with the ‘assumption’ that humanness must be explained in terms of genetic change. This assumption is not fact. The neo-Darwin genetic assumption does not seem to fit the known facts and it certainly hasn’t led to any useful explanations.
One of the fundamental complaints against evolutionary theory is that there are no major examples of evolutionary change available for study. If you substitute the neo-Darwin assumption for the more realistic alternatives suggested above, then the ‘evolution of humanness’ will be recognized as a ‘major ongoing evolutionary change’.
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Evan
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Member # 164
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posted 29. May 2002 10:07
Warren writes, "3. Human creative intelligence continues to evolve rapidly." I have seen him make statements like this in other posts.
I think this is a highly dubious proposition.
I see little evidence in the world to justify the statement that the overall creative intelligence of human beings is changing rapidly, much less evolving in the sense of becoming a fixed biological property of human beings.
Knowledge is increasing rapidly, of course, and has done so more or less exponentially since the start of civilization and the invention of writing. But I don't think that human beings are any more intelligent, in general, now than they were then, much less "creatively" intelligent (whatever that might mean.)
It seems to me Warren has confused accumulated cultural knowledge, transmitted through education and knowledge, with the capabilities of the individual. If somehow all the structures of civilization were suddenly removed and modern humans were transported to a stone-age society, they would, I think, handle their lives no differently (intelligently or otherwise) than the stone-age people of 40,000 years ago did at that time.
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Zia H. Shah
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Member # 284
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posted 29. May 2002 10:08
Dear Warren
May be I do not fully understand your message. Won't you think that in this day and age of cloning, if we can make a human from human genome and a chimpanzee from the chimpanzee genome then the difference between the two lies in the differences between the genomes.
I do hope that in this thread we can focus on the genetic differences between the two species and if there are mechanisms intelligent (artificial or real) or otherwise to explain that.
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Zia H. Shah
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Member # 284
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posted 29. May 2002 10:14
Dear Evan
I whole heartedly agree with your post.
However, once again, I hope that this thread will evolve in the direction of differences between the two genomes.
There is a Chimpanzee Genome Project, which will be developing the information about the genome in line with the Human Genome Project and they have a web site also.
Granted that we may not know these genomes in full details, but I hope we can have a theoretical discussion about the possible or proposed differences between the genomes.
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warren_bergerson
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Member # 262
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posted 29. May 2002 11:29
Zia,
This is your thread, and I don’t want to move the topic off the track you intended. I will just note that the ‘humans from human genes’ argument does not preclude the possibility that ‘humanness’ is a non-genetic trait or that human creative intelligence can evolve independent of changes in the genetic make up of individuals. If, as I suggest, human creative intelligence involve ‘human social behavior’ rather than ‘individual behavior’, then the assumptions I propose are logically possible. But, that is not the topic you are interested in so I’ll let it drop.
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James A. Barham
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Member # 50
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posted 29. May 2002 12:11
I think there are two very separate issues being confused on this thread.
(1) What, in general, is the relation between genotype and phenotype?
(2) What, in particular, accounts for the difference between us and our closest primate cousins?
As to (1), there is a lot of backlash going on right now against the assumptions of genetic reductionism, in many different areas of science. My favorite example is the way the tone of discussion in the popular press about the Human Genome Project has changed. A few years ago, this was going to be the key to life and solve all our problems. Now, it is just a big database that we have little idea what to do with. So, now we have to push for the Human Proteome Project (identifying all proteins), or beyond that, the Human Physiome Project (how the proteins interact). About the earlier silly hype, there is a deafening silence.
Several new books discuss the complexity of the genotype/phenotype relation in detail (e.g., S. Oyama et al., eds., Cycles of Contingency, MIT Press, 2001; E. Avital & E. Jablonka, Animal Traditions, Cambridge UP, 2000), so I won't go into it here. But one example I like to use is the following. Bears can learn to ride bicycles. Does this mean we must posit a latent gene (an "exaptation", perhaps) for "ursine cyclism"?
As for (2), I personally think that most of what we consider as unique about human nature is due to language, which of course begs the question of how language is possible. But whatever the neural basis of language ultimately turns out to be, I assume it will fit comfortably within the 2% (if that is really what it is).
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Johan de Boer
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Member # 287
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posted 29. May 2002 14:13
James -- I think that your statement
"My favorite example is the way the tone of discussion in the popular press about the Human Genome Project has changed."
is telling. The popular press is not exactly an authority! The genome is just the code for all the proteins as well as being involved in the regulation of their expression. How the proteins interact and what they do is a different matter entirely, and much more difficult to unravel, as is just now being started by proteome and interactome analysis. This is where the real understanding may come. Small differences in genome sequences can have profound effects through these levels. Determining the genome sequence is just the foundation for this understanding, a required step by itself but only useful for the next step and for medical diagnosis.
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Zia H. Shah
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Member # 284
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posted 29. May 2002 14:41
James
You said
"I personally think that most of what we consider as unique about human nature is due to language, which of course begs the question of how language is possible. But whatever the neural basis of language ultimately turns out to be, I assume it will fit comfortably within the 2% (if that is really what it is)."
This is a very helpful statement. We are beginning to focus on the key phenotype difference between the chimpanzees and humans that is the language. The development of intellect may go hand in hand with the development of language. I also appreciate your assumption that as regards the genotype the difference may lie in the different 2%.
In addition to these nice observations, I hope that you and other members will speculate on as to how the difference of 2% could come about in the period of 2-3 million years between chimpanzees and first humans. I have proposed one possible mechanism in the original post in this thread. We of course need explanation by an "Intellignet Design", but we know that Intelligent Being (e.g. God) executes plans through mechanisms, which can then be studied by other intelligent beings (e.g. humans)
Incidently, I did order the book, that you suggested, Cycles of Contingency, through Amazon.
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YZ2
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Member # 91
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posted 05. June 2002 23:11
I have speculations about the similarity between the human's and the chimpanzee's genome:
1) Their similarity is mostly a reflection of the similarity of their biological functions, rather than their phylogeny. Since chimpanzees and humans have a lot in common, so it is not surprising to see their genomes are also similar.
2) 2% of the genome has quite a large capacity for information storage, especially when the difference is placed at strategic points in the genome. I do not see why it cannot be accountable for the differences between humans and chimpanzees.
3) Obviously, the genome may not be everthing that account for the species. This is the age-old discussion beween nature and nurture. I see proteomics etc. are the studies related to understanding how the genome interacts with the environments. Thus understanding the genome is still very important in these studies.
4) James has pointed out that understanding the genome's relationship to the biological functions (and phenotypes) is still largely unsolved. Perhaps. But it does not mean that its understanding is irrelevant to science or philosophy. My gut feeling is that it can be done and is progressing.
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nobody
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Member # 145
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posted 28. June 2002 14:53
Zia H. Shah says:
"It would be important for our organization to support research projects on finding additional functions in the so-called “Junk DNA”. There in may lie the ultimate answers. Discovering, selection mechanisms (artificial intelligence) in the DNA will move our debate with the Darwinians from theoretical to pragmatic grounds and will serve the cause of science and research at the same time. If we find such artificial intelligence in genomes then our debate will shift to how some real intelligence put such artificial intelligence in the system."
What organization do you refer to? ISCID?
I'm not sure you will find any additional functions in the so-called “Junk DNA”. It does not seem to be a hot area of research. Personally I do not like calling any of God's designs "junk".
I also do not think that you will find artificial intelligence in DNA. I think what we see is highly sophisticated programming. Programming that is beyond our current capability. I think that's an obvious sign of a Creator/Designer/Programmer.
If you have not seen it before, this site has some very good information:
http://doegenomestolife.org/roadmap/grn.html
"Gene regulatory networks (GRNs) are the on-off switches and rheostats of a cell operating at the gene level. They dynamically orchestrate the level of expression for each gene in the genome by controlling whether and how vigorously that gene will be transcribed into RNA. Each RNA transcript then functions as the template for synthesis of a specific protein by the process of translation. A simple GRN would consist of one or more input signaling pathways, regulatory proteins that integrate the input signals, several target genes (in bacteria a target operon), and the RNA and proteins produced from those target genes. In addition, such networks often include dynamic feedback loops that provide for further regulation of network architecture and output. As indicated in the schematic below, input signaling pathways transduce intracellular and/or extracellular signals to a group of regulatory proteins called transcription factors. Transcription factors activated by the signals then interact, either directly or indirectly, with DNA sequences belonging to the specific genes they regulate. The factors also interact with each other to form multiprotein complexes bound to the DNA.
GRNs act as analog biochemical computers to specify the identity and level of expression of groups of target genes."
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warren_bergerson
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Member # 262
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posted 28. June 2002 18:07
Nobody,
QUOTE: GRNs act as analog biochemical computers to specify the identity and level of expression of groups of target genes."
It would be more accurate to say the GRN’s define the programs that keep a cell in an adaptive state at a point in time. The interesting question is the ‘intelligent computer’ that is continually reprogramming GRN’s in trillions of cells in order to keep not only individual cells in adaptive states, but to coordinate these adaptive states so the entire organism is in an adaptive state.
GRN’s don’t just change magically. There must be very complex processes in nature which are responsible for producing the required adaptive or teleological states.
It is, IMO, amazing how much knowledge is being accumulated in this area, and how relatively little success they seem to have in the purposeful, adaptive or teleological change that is obviously occurring.
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Frances
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Member # 169
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posted 28. June 2002 23:58
Warren
quote:
It is, IMO, amazing how much knowledge is being accumulated in this area, and how relatively little success they seem to have in the purposeful, adaptive or teleological change that is obviously occurring.
That seems to be begging the question. First of all purposeful is hardly in contradiction with evolution since purpose can be assigned after the fact. As far as adaptive is concerned, I have not seen much evidence that there are adaptive changes in the sense of adaptive mutations, other than in the sense of increased mutations rates. And as far as teleology is concerned, I have seen even less evidence for such.
It would be very helpful to me if Warren would present us some references for these? This would surely facilitate the discussion
[ 29 June 2002, 14:00: Message edited by: Frances ]
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Frances
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Member # 169
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posted 29. June 2002 00:36
There is an article which suggests that Human or Chimp? 50 Genes Are the Key
quote:
It is a serious puzzle for biologists to explain how two such similar genetic programs generate such different animals. Dr. David L. Nelson, a biologist at the Baylor College of Medicine, said that some of the anatomical differences between chimps and humans might arise from very small changes in the genes that regulate fetal development.
We shall see if their predictions hold
The following paper suggest genetic differences between chimp/human
There seems to be at least a chromosomal count difference.
To understand the similarity we should listen to
this commentary
quote:
"How can this be?" Ridley continues. "The differences between me and a chimp are immense. It is hairier, it has a different shaped head, a different shaped body, different limbs, makes different noises. There is nothing about chimpanzees that looks ninety-eight percent like me. Oh really? Compared with what?... If you took two Plasticene amoebae and turned one into a chimpanzee, the other into a human being, almost all the changes you would make would be the same. Both would need thirty-two teeth, five fingers, two eyes, four limbs and a liver.... There is no bone in the chimpanzee body that I do not share. There is no known chemical in the chimpanzee brain that cannot be found in the human brain. There is no known part of the immune system, the digestive system, the vascular system, the lymph system or the nervous system that we have and chimpanzees do not, or vice versa. There is not even a brain lobe in the chimpanzee brain that we do not share."
The most interesting paper I have read so far is about the similarity between chimps and humans versus other apes
It's remarkable how similar we seem to be to our 'cousins'. Will the 2% be an over or under estimate of the genetic differences? Time shall tell us. Actually numbers suggest 1.2% difference in nucleotide sequence divergence. Since the split is thought to have happened 5-6 million years ago, is this 1.2% difference really unsurmountable?
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Moderator
Administrator
Member # 1
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posted 29. June 2002 08:37
Frances,
I understand your desire for concrete details, references, etc. However, I have noticed a harrassing and provoking tone lately in some of your interactions with warren_bergerson. I expect that you will treat him with dignity and respect even if you disagree with his ideas.
Thanks,
The ISCID Moderator
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