Genomics News

Human and yeast genes interchangeable after a billion years

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From The Scientist :

A large number of human genes can substitute for their defective counterparts in yeast and prevent the microorganisms from dying, according to a paper published today (May 21) in Science. Of more than 400 human-to-yeast gene replacements performed, almost 50 percent were effective at compensating for a missing vital function.
“No one has carried out an evolutionary study of this kind before and certainly not of this scale,” said Nevan Krogan of the University of California, San Francisco, who was not involved in the work. “It’s rather satisfying to see that half of the genes could complement [the yeast function] because it justifies continuing working in yeast as a model . . . to help understand human genes.”

In short, Darwin was wrong. Species do not just continue to diverge, via natural selection acting on random mutation.

It appears that if a process as a whole has diverged between yeast and humans, then its proteins “have all changed together,” said Madan Babu of the Medical Research Council Laboratory of Molecular Biology in the U.K., who was not involved in the work. “If you can’t replace some of the subunits of the DNA repair machinery, then you can’t replace any of them.”

There has got to be a better model for the genome than the one that the tenured Darwin profs have stuck us with.

Abstract: To determine whether genes retain ancestral functions over a billion years of evolution and to identify principles of deep evolutionary divergence, we replaced 414 essential yeast genes with their human orthologs, assaying for complementation of lethal growth defects upon loss of the yeast genes. Nearly half (47%) of the yeast genes could be successfully humanized. Sequence similarity and expression only partly predicted replaceability. Instead, replaceability depended strongly on gene modules: Genes in the same process tended to be similarly replaceable (e.g., sterol biosynthesis) or not (e.g., DNA replication initiation). Simulations confirmed that selection for specific function can maintain replaceability despite extensive sequence divergence. Critical ancestral functions of many essential genes are thus retained in a pathway-specific manner, resilient to drift in sequences, splicing, and protein interfaces. (paywall) – A.H. Kachroo et al., “Systematic humanization of yeast genes reveals conserved functions and genetic modularity,” Science, 348:921-25, 2015.

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12 Replies to “Human and yeast genes interchangeable after a billion years

  1. 1
    Mung says:

    Next they’ll be wanting to give human rights to Yeats.

  2. 2
    Axel says:

    Well, he was a great poet, Mung.

  3. 3
    ppolish says:

    “functional conservation despite a billion years of divergent evolution.”

    That’s quite a divergence. That’s quite a conservation.

    Somehow I don’t mind sharing common bits with Baker’s Yeast. Not as offensive to me as sharing common bits with Monkeys.

    “Oh, but DNA was just a accident. Not unique. Could have been something else.” Fail.

  4. 4
    Zachriel says:

    ppolish: Somehow I don’t mind sharing common bits with Baker’s Yeast. Not as offensive to me as sharing common bits with Monkeys.

    Nonetheless, you share more with the monkey than yeast, and most every commonality between you and yeast is also common between the monkey and yeast (nesting).

  5. 5
    ppolish says:

    Thanks Zach. Learn something new every day.

  6. 6
    bornagain77 says:

    On Human Origins: Is Our Genome Full of Junk DNA? Pt 2. – Richard Sternberg PhD. Evolutionary Biology
    Excerpt: “Here’s the interesting thing, when you look at the protein coding sequences that you have in your cell what you find is that they are nearly identical to the protein coding sequences of a dog, of a carp, of a fruit fly, of a nematode. They are virtually the same and they are interchangeable. You can knock out a gene that encodes a protein for an inner ear bone in say a mouse. This has been done. And then you can take a protein that is similar to it but from a fruit fly. And fruit flies aren’t vertebrates and they certainly are not mammals., so they don’t have inner ear bones. And you can plug that gene in and guess what happens? The offspring of the mouse will have a perfectly normal inner ear bone. So you can swap out all these files. I mentioning this to you because when you hear about we are 99% similar (to chimps) it is almost all referring to those protein coding regions. When you start looking, and you start comparing different mammals. Dolphins, aardvarks, elephants, manatees, humans, chimpanzees,, it doesn’t really matter. What you find is that the protein coding sequences are very well conserved, and there is also a lot of the DNA that is not protein coding that is also highly conserved. But when you look at the chromosomes and those banding patterns, those bar codes, (mentioned at the beginning of the talk), its akin to going into the grocery store. You see a bunch of black and white lines right? You’ve seen one bar code you’ve seen them all. But those bar codes are not the same.,, Here’s an example, aardvark and human chromosomes. They look very similar at the DNA level when you take small snippets of them. (Yet) When you look at how they are arranged in a linear pattern along the chromosome they turn out to be very distinct (from one another). So when you get to the folder and the super-folder and the higher order level, that’s when you find these striking differences. And here is another example. They are now sequencing the nuclear DNA of the Atlantic bottle-nose dolphin. And when they started initially sequencing the DNA, the first thing they realized is that basically the Dolphin genome is almost wholly identical to the human genome. That is, there are a few chromosome rearrangements here and there, you line the sequences up and they fit very well. Yet no one would argue, based on a statement like that, that bottle-nose dolphins are closely related to us. Our sister species if you will. No one would presume to do that. So you would have to layer in some other presumption. But here is the point. You will see these statements throughout the literature of how common things are.,,, (Parts lists are very similar, but how the parts are used is where you will find tremendous differences)
    http://www.discovery.org/multi.....-dna-pt-2/

    Genetic Evolution Falsified – May 23, 2015
    Excerpt: To study this effect systematically, Kachroo et al. replaced over 400 essential yeast genes with their human orthologs. Roughly half of the human genes could functionally replace their yeast counterparts. Genes being in the same pathway was as important as sequence or expression similarity in determining replaceability. ,,,
    New Scientist says that it’s not just yeast. Studies of genes in ocean plankton caused the same stunned response by an evolutionist:
    We’re a step closer to understanding the microbial community that inhabits the ocean — and it has some striking similarities to the community that lives inside our guts. The microbiome of the world’s biggest ecosystem and one of the smallest appear to function in surprisingly similar ways.…
    In both, there was an almost identical abundance of genes involved in replication, ion transport and cell motility.
    “This certainly was rather a big surprise to us because we expected different ecosystems would have microbial communities with functions that would be completely different,” Sunagawa said at a press conference this week.
    If prediction is a measure of scientific validity of a theory, this amounts to a falsification. This “certainly” was not what the evolutionists expected.
    http://crev.info/2015/05/genet.....falsified/

    Evolution by Splicing – Comparing gene transcripts from different species reveals surprising splicing diversity. – Ruth Williams – December 20, 2012
    Excerpt: A major question in vertebrate evolutionary biology is “how do physical and behavioral differences arise if we have a very similar set of genes to that of the mouse, chicken, or frog?”,,,
    A commonly discussed mechanism was variable levels of gene expression, but both Blencowe and Chris Burge,,, found that gene expression is relatively conserved among species.
    On the other hand, the papers show that most alternative splicing events differ widely between even closely related species. “The alternative splicing patterns are very different even between humans and chimpanzees,” said Blencowe.,,,
    http://www.the-scientist.com/?.....plicing%2F

    “Where (chimps and humans) really differ, and they differ by orders of magnitude, is in the genomic architecture outside the protein coding regions. They are vastly, vastly, different.,, The structural, the organization, the regulatory sequences, the hierarchy for how things are organized and used are vastly different between a chimpanzee and a human being in their genomes.”
    Raymond Bohlin (per Richard Sternberg) – 9:29 minute mark of video
    https://vimeo.com/106012299

    A Listener’s Guide to the Meyer-Marshall Debate: Focus on the Origin of Information Question -Casey Luskin – December 4, 2013
    Excerpt: “There is always an observable consequence if a dGRN (developmental gene regulatory network) subcircuit is interrupted. Since these consequences are always catastrophically bad, flexibility is minimal, and since the subcircuits are all interconnected, the whole network partakes of the quality that there is only one way for things to work. And indeed the embryos of each species develop in only one way.” –
    Eric Davidson
    http://www.evolutionnews.org/2.....79811.html

    Thus, where Darwinists most need plasticity in the genome to be viable as a theory, (i.e. developmental Gene Regulatory Networks), is the place where mutations are found to be ‘always catastrophically bad’. Yet, it is exactly in this area of the genome (i.e. regulatory networks) where substantial, ‘orders of magnitude’, differences are found between even supposedly closely related species.
    Needless to say, this is the exact opposite finding for what Darwinism would have predicted for what should have been found in the genome.

  7. 7
    ppolish says:

    I don’t think you understand monkeys, BA. You should ask Zach – he seems knowledgable on monkeys.

  8. 8
    Querius says:

    One minor correction, ppolish. Chimpanzees are considered apes rather than monkeys, which generally have tails.

    Now that Chimpanzees are becoming widely regarded as having 102% identical DNA as humans, it explains the quote from a Science magazine article by Ann Gibbons (sic) who quotes an astonished computational biologist Janet Kelso of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany:

    We’re so closely related genetically, yet our behavior is so different. This will allow us to look for the genetic basis of what makes modern humans different from both bonobos and chimpanzees

    The key differences are apparently behavioral! The article continues with another amazing revelation about a difference between humans, bonobos, and chimpanzees:

    Another difference is that bonobos and humans, but not chimps, have a version of a protein found in urine that may have similar function in apes as it does in mice, which detect differences in scent to pick up social cues.

    Exactly. In humans this usually results in verbalization of something like, “Hey, what’s that smell? Look everyone, Jimmy laughed so hard, he wet himself!”

    This has prompted researchers to speculate whether the ancestor of humans, chimpanzees, and bonobos looked and acted more like a bonobo, a chimpanzee, or something else

    This means that the most recent common ancestor between chimpanzees, humans, and bonobos might well have most closely resembled humans!

    http://news.sciencemag.org/pla.....-relatives

    -Q

  9. 9
    ppolish says:

    Modern chimps and bonobos are very recent descendants of ancient human forms? Well, I’ll be a monkey’s uncle. That would certainly explain the lack of chimp and bonobo in the fossil record. Lack of all apes gasp.

    “But chimps and bonobos are too delicate to fossilize. Like Precambrian soft tissue critters.”

    No. Like soylent green – Apes is people!

  10. 10
    ppolish says:

    Chimps have 99% human DNA. They are like our “mentally challenged” uncles. Not polite to say “retarded” anymore. But deep down all chimps are human like. We are all Africans.

  11. 11
    bornagain77 says:

    Guy Walks Into a Bar and Thinks He’s a Chimpanzee: The Unbearable Lightness of Chimp-Human Genome Similarity – Sternberg – 2009
    Excerpt: One can seriously call into question the statement that human and chimp genomes are 99% identical. For one thing, it has been noted in the literature that the exact degree of identity between the two genomes is as yet unknown (Cohen, J., 2007. Relative differences: The myth of 1% Science 316: 1836.). ,,, In short, the figure of identity that one wants to use is dependent on various methodological factors.
    http://www.evolutionnews.org/2.....think.html

    The Chimp-Human 1% Difference: A Useful Lie – 06/29/2007
    Excerpt: But truth be told, Wilson and King also noted that the 1% difference wasn’t the whole story. They predicted that there must be profound differences outside genes—they focused on gene regulation—to account for the anatomical and behavioral disparities between our knuckle-dragging cousins and us. Several recent studies have proven them perspicacious again, raising the question of whether the 1% truism should be retired.
    “For many, many years, the 1% difference served us well because it was underappreciated how similar we were,” says Pascal Gagneux, a zoologist at UC San Diego. “Now it’s totally clear that it’s more a hindrance for understanding than a help.”,,,
    This is a very disturbing article. We have basically caught the Darwinists in a bald lie that has hoodwinked the world for over 30 years. Gagneux says, “For many, many years, the 1% difference served us well” – stop right there! Who is “us”? Was it the millions of school children and laymen who were lied to? Was it the majority of people who believe God created mankind, suffering under an onslaught of lies told in the name of science? No! “Us” refers to the members of the Darwin Party,,,
    http://creationsafaris.com/cre.....#20070629a

    Chimp DNA Mutation Study—Selective Yet Surprising – Jeffrey Tomkins – August 16, 2014
    Excerpt: It was initially noted by another group of evolutionary scientists that when comparing random chimp genomic sequence only “about two thirds could be unambiguously aligned to DNA sequences in humans”(2). In confirmation of this widely known, but seldom discussed, inconvenient fact among those evolutionists working in the field was a comprehensive study published in 2013 by this author (3). In that research, I compared each individual chimpanzee chromosome to human (piece-by-piece) and it was shown that the chimpanzee genome was only 70% similar on average to human, with only short regions being highly similar.
    ,,, 30% difference in their genomes—some 900,000,000 DNA letter differences.,,,
    When the entire genomes are compared between humans and chimps, it becomes clear that they were each engineered uniquely and separately by an Omnipotent Creator.
    http://www.designed-dna.org/bl.....c5-110.php

    Geneticist Jeff Tomkins vs. Evolutionary Biologist who got laughed off stage – August 12, 2013
    Excerpt: Tomkins described the origin of the fallacious comparison as a myth that got started in reassociation kinetic methods of comparison in the mid-1970’s prior to the advent of modern sequencing techniques (like Illumina and Solexa). Reassociation kinetics was a technique where fragments of chimp and human DNA were mixed in the same chemical soup, and the DNAs that were reasonably similar would pair up, hence we got a biased sampling!
    If we take genes that are found in both humans and chimps and disregard the indels, we get the 98% figure. When indels are considered, the similarity drops to 80-85%!
    When including other sequences, the similarity drops even further, down to 70%. But that 70% figure itself, imho, is too generous. I don’t think Tomkins used ORFans or pseudo genes or many other intergenic sequences, and he explicitly avoided the complication of Synteny….
    Tomkins pointed also to reports where lab workers may have contaminated the sequencing labs for Chimps with their own human DNA and thus biasing the figures! Hence re-sequencing has been done, and there is more sequencing pending to clean up these errors. He joked about the coughing and sneezing that may have gone on to cause contamination.
    http://www.uncommondescent.com.....off-stage/

    Human and Chimp DNA–Nearly Identical? by Jeffrey Tomkins, Ph.D. – 2014
    Excerpt: Major research published over the past decade comparing human and chimpanzee DNA was recently reviewed and critiqued.1 In every single publication, researchers only reported on the highly similar DNA sequence data and discarded the rest—apparently because it was too dissimilar. In fact, when the DNA similarities from these studies were recalculated using the omitted data, markedly lower levels—between 81 and 86 percent similarity—were found. Even the well-known chimpanzee genome paper published by evolutionists in 2005 provides a genomic similarity of only about 80 percent when the discarded nonsimilar data are included and only 70 percent when the estimated size of the chimpanzee genome is incorporated.2,3,,,
    Not counting the Y-chromosome, the results of my comparison showed variability between 66 and 76 percent similarity for the different chimp chromosomes, with an overall genome average of only 70 percent similarity to human chromosomes. In reality, many chromosomal regions are vastly different between chimps and humans, and several areas of the genome that are present in chimps are completely absent in humans—and vice versa.
    While it is true that there are sections of the chimp genome that are very similar to humans, this is not the complete picture. DNA sequence comparisons that include all the relevant data plainly show that the human and chimp genomes are not nearly identical at all. Instead, they are as distinct as one might expect based on the obvious differences in the resulting anatomies and behavioral capacities.
    Hypothetical evolutionary processes cannot explain the extremely broad differences between chimp and human DNA when the whole genomes are considered. The similar regions between genomes are easily interpreted as the basic reuse of effective code—a concept very familiar to software engineers.,,,
    http://www.icr.org/article/7892/

    Comprehensive Analysis of Chimpanzee and Human Chromosomes Reveals Average DNA Similarity of 70% – by Jeffrey P. Tomkins – February 20, 2013
    Excerpt: For the chimp autosomes, the amount of optimally aligned DNA sequence provided similarities between 66 and 76%, depending on the chromosome. In general, the smaller and more gene-dense the chromosomes, the higher the DNA similarity—although there were several notable exceptions defying this trend. Only 69% of the chimpanzee X chromosome was similar to human and only 43% of the Y chromosome. Genome-wide, only 70% of the chimpanzee DNA was similar to human under the most optimal sequence-slice conditions. While, chimpanzees and humans share many localized protein-coding regions of high similarity, the overall extreme discontinuity between the two genomes defies evolutionary timescales and dogmatic presuppositions about a common ancestor.
    http://www.answersingenesis.or.....chromosome

    The Myth of 98% Genetic Similarity (and Chromosome Fusion) between Humans and Chimps – Jeffrey Tomkins PhD. – video
    https://vimeo.com/95287522

  12. 12
    M. Holcumbrink says:

    In other news: UN threaded bolts can be used in place of UNJ bolts for many aerospace applications with negligible effects. Engineers not really all that shocked.

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