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Author Topic:   Micro v. Macro Creationist Challenge
CRR
Member (Idle past 2242 days)
Posts: 579
From: Australia
Joined: 10-19-2016


(1)
Message 132 of 252 (814603)
07-11-2017 6:09 AM
Reply to: Message 83 by Faith
07-10-2017 4:10 AM


Re: Science means knowledge, period.
"Science" simply means "knowledge,"
It's a bit more than just knowledge. Consider these five possible definitions:-
(1) Science is nothing else than the search to discover unity in the wild variety of nature (J. Bronowski).
(2) The business of science is to find uniformities, such as the laws of motion and the law of gravitation, to which, so far as our experience extends, there are no exceptions (B. Russell).
(3) Falsifiability is the criterion of demarcation between science and non-science (K. Popper).
(4) What is science? At its core, science is observation. . . . science is empiricism (D. Breese).
(5) Science involves observation, using one or more of our five senses, to gain cumulative knowledge about the world and to be able to repeat the observations (K. Ham).
However we can't agree on a definition of the Theory of Evolution so it's unlikely the broader subject of science will fare better. For a start we would have to differentiate between Origins vs Operational science.
But why does science work? According to C.S. Lewis: Science began with belief in a Lawmaker
‘Men became scientific because they expected Law in Nature, and they expected Law in Nature because they believed in a Legislator. In most modern scientists this belief has died: it will be interesting to see how long their confidence in uniformity survives it. Two significant developments have already appearedthe hypothesis of a lawless sub-nature, and the surrender of the claim that science is true. We may be living nearer than we suppose to the end of the Scientific Age.’
Lewis, C.S., Miracles: a preliminary study, Collins, London, p. 110, 1947.

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CRR
Member (Idle past 2242 days)
Posts: 579
From: Australia
Joined: 10-19-2016


Message 143 of 252 (814710)
07-12-2017 1:20 AM


Michael Faraday and James Clerk Maxwell
Michael Faraday
Even though Darwin published his work on evolution near the end of Faraday’s life, several very good reasons exist to conclude that Faraday rejected Darwinism. In 1859 Darwin published his book The Origin of Species, which many have seen as undermining such a confident faith. The remarkable thing is that Faraday says nothing about evolution that implies any kind of unresolvable problem. Though by now his physical condition was deteriorating, he could think clearly for much of his time and express himself eloquently where that was necessary. His silence on Darwin’s work is highly significant. Like many physical scientists, he may have dismissed evolution as only a theory. More probably his faith was so strong that nothing, even in science, could shake it (Russell, 2000, p. 115).
Actually, Faraday said much about his religious beliefs, and Darwinism was directly contrary to his core beliefs, a fact that Faraday was no doubt keenly aware of. As one who interpreted the Bible as literally as possible, many students of science conclude that Faraday could not accept Darwinism. The teachings of his small fundamentalist church included a strong emphasis on God’s creation as
purposeful and harmonious, designed for man’s well-being. He had an abiding faith in the Bible and in prayer. Unlike Newton, however, he made little attempt to harmonize his science with his Biblical faith, supremely confident that the two were both based on divine truth and were necessarily in agreement. He fully believed in the official doctrine of his church, which said: The Bible, and it alone, with nothing added to it nor taken away from it by man, is the sole and sufficient guide for each individual, at all times and in all circumstances (Morris, Henry. 1988. Men of Science Men of God: Great Scientists Who Believed the Bible. Master Books. p. 37).
Michael Faraday: Christian and Scientist « Creation Science Association of Alberta
James Clerk Maxwell
Maxwell was widely read in theology. He interacted with many of the best theological minds of his day, always as a solid evangelical Christian. In fact, he often chided other believers for tying religious truth too tightly to the science of the day. He understood this not as a problem for God’s unchanging Word, but as a problem for man’s ever changing understanding of how the world works.
Maxwell’s faith in the Bible even shocked a young Karl Pearson who, when he questioned the Flood, was reprimanded by Maxwell for questioning the Bible!
The conversation turned on Darwinian evolution; I can’t say how it came about, but I spoke disrespectfully of Noah’s Flood. Clerk Maxwell was instantly aroused to the highest pitch of anger, reproving me for want of faith in the Bible! I had no idea at the time that he had retained the rigid faith of his childhood, and was, if possible, a firmer believer than Gladstone in the accuracy of Genesis.
Einsteins heroes - creation.com

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CRR
Member (Idle past 2242 days)
Posts: 579
From: Australia
Joined: 10-19-2016


Message 160 of 252 (815821)
07-24-2017 7:24 PM
Reply to: Message 159 by RAZD
07-13-2017 6:55 AM


Re: talk about off topic talk ...
You can always make up an evolutionary fairy tale to "explain" anything, particularly if you ignore real world constraints such time to fixity, and define microevolution broadly enough.
Since it includes included deletion as microevolution without any constraints as to size and rate then as I have said you can simply assume a common ancestor with hundreds of extra genes that got deleted in one or the other line leading to humans or chimps. There you are, all the non-homologous genes explained by microevolution. And the challenge is to show only a single change without considering concurrent changes..
Taq has set up the "challenge" up so that it can't fail. As such it is not worth the effort to attempt to meet it.
{Edit: Let me rephrase that, Taq has set up the "challenge" up so that it is no win. }
How about I propose an alternative?
Show that ALL of the genetic differences between humans and chimps could have been produced by microevolutionary processes within 10 million years using reasonable population sizes, mutation rates, generation times, and assuming that all the non-homologous genes have appeared since separation. Fitness effect of each change must be considered.
I would accept a gene duplication as a single evolutionary event
Explanation must include fusion of chromosome 2, differences between the human and chimp Y chromosome, and the loss or gain of a baculum.
Edited by CRR, : as marked

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CRR
Member (Idle past 2242 days)
Posts: 579
From: Australia
Joined: 10-19-2016


Message 162 of 252 (815970)
07-27-2017 7:42 AM
Reply to: Message 161 by Taq
07-25-2017 1:25 PM


Re: talk about off topic talk ...
I have no intention of trying to meet a no win challenge such as you have set up.
You might like to accept my challenge Message 1

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CRR
Member (Idle past 2242 days)
Posts: 579
From: Australia
Joined: 10-19-2016


Message 163 of 252 (815971)
07-27-2017 8:09 AM
Reply to: Message 161 by Taq
07-25-2017 1:25 PM


Re: talk about off topic talk ...
You haven't demonstrated that the new genes in the human lineage lack homologous sequence in the chimp genome.
By golly I haven't!
I guess I just took the word of geneticists on that one, such as Author Summary For the past 20 years scientists have puzzled over a strange-yet-ubiquitous genomic phenomenon; in every genome there are sets of genes which are unique to that particular species i.e. lacking homologues in any other species. How have these genes originated? The advent of massively parallel RNA sequencing (RNA-Seq) has provided new clues to this question, with the discovery of an unexpectedly high number of transcripts that do not correspond to typical protein-coding genes, and which could serve as a substrate for this process. Here we have examined RNA-Seq data from 8 mammalian species in order to define a set of putative newly-born genes in human and chimpanzee and investigate what drives their expression. This is the largest-scale project to date that tries to address this scientific question. We have found thousands of transcripts that are human and/or chimpanzee-specific and which are likely to have originated de novo from previously non-transcribed regions of the genome. We have observed an enrichment in transcription factor binding sites in the promoter regions of these genes when compared to other species; this is consistent with the idea that the gain of new regulatory motifs results in de novo gene expression. We also show that some of the genes encode new functional proteins expressed in brain or testis, which may have contributed to phenotypic novelties in human evolution. where the authors claim to have identified 634 human-specific genes and 780 chimpanzee-specific genes.
The more readable version is in Scientific American here
Of course the exact number is likely to change over time and I think some older sources report lower numbers.

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CRR
Member (Idle past 2242 days)
Posts: 579
From: Australia
Joined: 10-19-2016


Message 167 of 252 (816018)
07-27-2017 11:50 PM
Reply to: Message 166 by Taq
07-27-2017 12:00 PM


Human-chimp non homologues
Try these ones.
Homo sapiens genes vs Pan troglodytes
PLCXD1 (ENSG00000182378) No homologues
GTPBP6 (ENSG00000178605) No homologues
PPP2R3B (ENSG00000167393) No homologues
SHOX (ENSG00000185960) No homologues
CRLF2 (ENSG00000205755) No homologues
IL3RA (ENSG00000185291) No homologues
SLC25A6 (ENSG00000169100) No homologues
AKAP17A (ENSG00000197976) No homologues
ASMT (ENSG00000196433) No homologues
ZBED1 (ENSG00000214717) No homologues
Chromosome Y: 276,322-2,741,309 - Synteny - Homo_sapiens - Ensembl genome browser 107

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CRR
Member (Idle past 2242 days)
Posts: 579
From: Australia
Joined: 10-19-2016


Message 169 of 252 (816070)
07-28-2017 7:05 PM
Reply to: Message 168 by Taq
07-28-2017 10:49 AM


Re: Human-chimp non homologues
They were all listed as "no homologue" on the Encode website. Sorry, but I trust Encode more than you.

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 Message 168 by Taq, posted 07-28-2017 10:49 AM Taq has replied

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CRR
Member (Idle past 2242 days)
Posts: 579
From: Australia
Joined: 10-19-2016


Message 171 of 252 (816266)
08-02-2017 4:13 AM
Reply to: Message 161 by Taq
07-25-2017 1:25 PM


Re: Human-chimp non homologues
Taq writes:
You haven't demonstrated that the new genes in the human lineage lack homologous sequence in the chimp genome.
Do you accept that there are genes in humans that have no homologue in chimps?
Edited by CRR, : typo corrected
Edited by CRR, : Subtitle amended

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CRR
Member (Idle past 2242 days)
Posts: 579
From: Australia
Joined: 10-19-2016


Message 172 of 252 (816272)
08-02-2017 6:09 AM
Reply to: Message 170 by Taq
07-31-2017 10:52 AM


Re: Human-chimp non homologues
Taq writes:
Did ENCODE list them as human specific genes?
The link I provided compared them to the chimp genome only. Some of them would be human specific genes.
How many human specific genes are there? I don't know and neither does anyone else, however there ARE human specific genes as an internet search will show you. Such as Human-specific gene ARHGAP11B.
According to this Nature paper, every evolutionary lineage harbours orphan genes that lack homologues in other lineages and whose evolutionary origin is only poorly understood

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CRR
Member (Idle past 2242 days)
Posts: 579
From: Australia
Joined: 10-19-2016


Message 175 of 252 (816324)
08-02-2017 6:28 PM
Reply to: Message 174 by Taq
08-02-2017 11:02 AM


Re: Human-chimp non homologues
Strangely I put more weight on the papers published in Science and Nature than on your BLAT experiments. No doubt there is a lot more work to be done in this area and I might yet be disappointed but for now I will go with the scientific consensus. Hang in there, the scientific consensus has often been wrong. You might be able to publish your own paper showing how those other authors got it wrong.

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CRR
Member (Idle past 2242 days)
Posts: 579
From: Australia
Joined: 10-19-2016


Message 178 of 252 (816390)
08-03-2017 8:15 PM


Non homologous genes
Let's go back a bit.
Are there non homologous genes when comparing humans to chimps?
Ensemble website here shows many human genes as having no homologue anywhere in the chimp genome. (And many chimp genes that have no homologue in humans).
What does Ensemble mean when it says "no homologue"?
Edited by CRR, : No reason given.

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CRR
Member (Idle past 2242 days)
Posts: 579
From: Australia
Joined: 10-19-2016


Message 180 of 252 (816603)
08-07-2017 9:28 PM
Reply to: Message 179 by Taq
08-04-2017 10:48 AM


Re: Non homologous genes
CRR writes:
Let's go back a bit.
Are there non homologous genes when comparing humans to chimps?
I have no doubt that there could have been gene loss in either the chimp or human lineages. Do you think gene loss is an impediment to macroevolution? If not, then why mention it?
"The chimpanzee MSY [Y-chromosome] contains twice as many massive palindromes as the human MSY, yet it has lost large fractions of the MSY protein-coding genes and gene families present in the last common ancestor."
Ok I will take that as agreement that there are non homologous genes when comparing humans to chimps.
The explanation you seem to be advancing is that the non-homologous genes are explained by gene loss in both species. That is a possibility I have raised in the past. This would mean that the common ancestor had all those non-homologous genes from both species. But don't stop there. The common ancestor of all the great apes would have had all the genes of all the great apes. You can extend this as far back down the phylogenetic tree as you like.
What we see then is evolution by genetic loss. Then I guess it means that Microevolution is loss of genetic information in a population over time; and Macroevolution is when genetic loss results in morphological change and separation into new species, genera, etc.
However if you go back to my past posts you will find that I disagree with equating macroevolution to speciation. I have said that speciation could be the result of either microevolution or macroevolution; where the critical difference is whether the mutation adds a significant amount of new genetic information.
A BLAT search also finds homologous DNA (first 1,000 bp) on the chimp X-chromosome for PLCXD1, the first gene on your Ensembl list below.
I think that's about 4% of PLCXD1. As I've said before I think I will put more weight on the Ensemble assessment of whether genes are homologous or not.

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CRR
Member (Idle past 2242 days)
Posts: 579
From: Australia
Joined: 10-19-2016


Message 183 of 252 (816660)
08-09-2017 3:52 AM
Reply to: Message 181 by Percy
08-08-2017 7:47 AM


Re: micro/macro definitions
There's a whole topic in that. The issue remains unresolved. I favour Durston's definitions myself.
[edit] Or from Message 107
microevolution = changes in gene frequencies and trait distributions that occur within populations and species
macroevolution = large evolutionary change, usually in morphology, typically refers to evolution of differences among populations that would warrant their plaecment in different genera or higher-level taxa
Edited by CRR, : [edit] Or from Message 107

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CRR
Member (Idle past 2242 days)
Posts: 579
From: Australia
Joined: 10-19-2016


Message 184 of 252 (816661)
08-09-2017 4:31 AM
Reply to: Message 182 by Taq
08-08-2017 12:35 PM


Re: Non homologous genes
So for human genes that have no homologue in the chimp genome the explanation is gene loss in the chimp lineage, but not in the human lineage.
The Chimp genome has many genes that have, according to Ensemble, no homologue in the Human genome.
Is the explanation for this gene loss in the human lineage, but not in the chimp lineage?

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CRR
Member (Idle past 2242 days)
Posts: 579
From: Australia
Joined: 10-19-2016


Message 188 of 252 (816711)
08-09-2017 6:41 PM
Reply to: Message 186 by Taq
08-09-2017 10:41 AM


Re: Non homologous genes between humans and chimps
Right now I'm focusing on non-homologous genes between humans and chimps. The Ensemble pages I linked previously show that humans have many genes that have no homologue anywhere in the chimp genome. You have already stated that the best explanation is gene loss in the chimp lineage, but not in the human lineage.
The Ensemble site also shows that chimps have many genes that have no homologue anywhere in the human genome. What do you think is the best explanation for this? Is it gene loss in the HUMAN lineage, but not in the CHIMP lineage?
We can look at orthologues later.

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