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Why you are fat and the chimp isn’t

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File:A small cup of coffee.JPG Explained at Real Clear Science:

As a genus, humans, from Homo sapiens (that’s us) to our extinct ancestors Homo neanderthalensis and Homo erectus, are wanderers. Over the vast majority of our history, which spans hundreds of thousands of years, we have roved from place to place, inhabiting a wide range of habitats. We moved with the seasons, we moved to find food, we moved — perhaps — just to move. Our adaptability was our key adaptation, an evolutionary leg-up on the competition. The ability to store fat was vital to this lifestyle. Body fat cushions internal organs, but it also serves as a repository of energy that can be readily broken down and used to power muscles. Humans might fatten up at one environment, then move on to another. When food was scarce, we could count on our fat to sustain us, at least temporarily.

Chimpanzees, on the other hand, are localized to specific environments where food is often plentiful, primarily the forests of West and Central Africa. Fatty stores of energy aren’t required, but strength to climb food-bearing trees is. Natural selection favored brawn, causing chimps to shed fat as unnecessary weight.

Clever idea. But thoughts from readers?

(Who would want to be a chimp just to be thin?)

See also: Why human evolution did not go the way analysts would have predicted

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Comments
wd400: Lol.
Nice to see some self-mockery from a proponent of a group of people who often take themselves too seriously.Box
June 8, 2015
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Silver Asiatic: Because that’s the way they were designed. Sure. Synonymous substitutions were designed for no other reason than to look like common descent. Silver Asiatic: The explanation for why that feature developed in mammals is an exercise in story-telling. It's an example of how posited convergence still leaves the overall nesting pattern intact. It contradicts bornagain77's and your contention that convergence “reflects a breakdown" in nesting. Darwin: It is incredible that the descendants of two organisms, which had originally differed in a marked manner, should ever afterwards converge so closely as to lead to a near approach to identity throughout their whole organisation.Zachriel
June 8, 2015
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Lol.wd400
June 8, 2015
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Zach
While fish and whales both have slippery surfaces (convergence)
The explanation for why that feature developed in mammals is an exercise in story-telling.Silver Asiatic
June 8, 2015
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wd400
Why do the synonymous mutations in Prestin make a tree that perfectly matches the mammal tree estimated from the rest of the genome?
Because that's the way they were designed.Silver Asiatic
June 8, 2015
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Silver Asiatic: As BA pointed out, with convergent evolution that assumption breaks down. Even with convergence, you can still determine a consistent nested pattern. While fish and whales both have slippery surfaces (convergence), anything but a cursory look will reveal that whales group with mammals (nested). Silver Asiatic: That they could not estimate the probability of (and therefore cannot predict) the occurrence of the non-synonymous substitutions. Synonymous substitutions support the standard mammalian phylogeny.Zachriel
June 8, 2015
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Actually your numbers are way off wd400: Whale Evolution Vs. Population Genetics - Richard Sternberg PhD. in Evolutionary Biology – video http://www.youtube.com/watch?v=85kThFEDi8o Evolution And Probabilities: A Response to Jason Rosenhouse - August 2011 Excerpt: The equations of population genetics predict that – assuming an effective population size of 100,000 individuals per generation, and a generation turnover time of 5 years – according to Richard Sternberg’s calculations and based on equations of population genetics applied in the Durrett and Schmidt paper, that one may reasonably expect two specific co-ordinated mutations to achieve fixation in the timeframe of around 43.3 million years. When one considers the magnitude of the engineering fete, such a scenario is found to be devoid of credibility. https://uncommondescent.com/intelligent-design/evolution-and-probabilities-a-response-to-jason-rosenhouse/ of related note: Convergent evolution' (homology in unexpected places) is found to be much more widespread than originally thought. Far more often than would be expected under the neo-Darwinian framework. "Despite its complexity, C4 photosynthesis is one of the best examples of 'convergent evolution', having evolved more than 50 times in at least 18 plant families (Sage 2004; Conway Morris 2006)." http://mbe.oxfordjournals.org/content/26/8/1909.full.pdf “The reason evolutionary biologists believe in "40 known independent eye evolutions" isn't because they've reconstructed those evolutionary pathways, but because eyes don't assume a treelike pattern on the famous Darwinian "tree of life." Darwinists are accordingly forced, again and again, to invoke convergent "independent" evolution of eyes to explain why eyes are distributed in such a non-tree-like fashion. This is hardly evidence against ID. In fact the appearance of eyes within widely disparate groups speaks eloquently of common design. Eyes are a problem, all right -- for Darwinism.” http://www.evolutionnews.org/2014/03/its_a_shame_rea083441.html , Simon Conway Morris has a website documenting hundreds, if not thousands, of examples of 'convergence': Map Of Life – Simon Conway Morris http://www.mapoflife.org/browse/ Simon Conway Morris: “Fossil evidence demands a radical rewriting of evolution.” – March 2012 Excerpt: “The idea is this: that convergence – the tendency of very different organisms to evolve similar solutions to biological problems – is not just part of evolution, but a driving force. To say this is an unconventional view would be something of an understatement.” https://uncommondescent.com/evolution/simon-conway-morris-fossil-evidence-demands-a-radical-rewriting-of-evolution/bornagain77
June 8, 2015
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Neither lineage developed echolocation "from" these mutations. If there are only a handful of mutaitons that can increase teh fidelity of high-frequency hearing via prestin then it's pretty likely two echolocating lineages will find them. Back on an envelope, say changing a Proline to a Histidine would be favoured in an echolocating lineage. Half of the second position mutations in a Pro codon will lead to His. Since the mutation rate is mammals is ~1e-8 that's a 5e-9 chance per-individual per-generation. With a population size of 10, 000 you'd get a rate of 5e-5 per generation and therefore an expected waiting time of ~20,000 generations. So the mutation would come up often enough, the fact it's favoured in both echolocating lineages would make it much more likely to become fixed. Precise calculations would require us to know about the way mutations interact with each other to create the phenotype and their respective selective advantages. Calculating the probability that each lineage would find the same substitutions would require us to know about what other mutations might have the same effects (or to turn it around,, this finding is evidence that only a few mutations are able to generate better high-frequency hearing). Now, answer my question. Why do the synonymous mutations in Prestin make a tree that perfectly matches the mammal tree estimated from the rest of the genome?wd400
June 8, 2015
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corrected link Picture: Echolocation in bats and whales based on same changes to same gene http://blogs.discovermagazine.com/notrocketscience/files/2010/01/echolocation_in_bats_and_whales_based_on_same_changes_to_sam/Prestin-tree.jpg The echolocation abilities of bats and whales, though different in their details, rely on the same changes to the same gene – Prestin. These changes have produced such similar proteins that if you drew a family tree based on their amino acid sequences, bats and toothed whales would end up in the same tight-knit group, to the exclusion of other bats and whales that don’t use sonar. http://blogs.discovermagazine.com/notrocketscience/2010/01/25/echolocation-in-bats-and-whales-based-on-same-changes-to-same-gene/#.VXXadkbcBCAbornagain77
June 8, 2015
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wd400 What was the probability that bats and whales would both develop echolocation from a common selection for amino-acid-altering mutations?Silver Asiatic
June 8, 2015
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Zach
but a nested pattern of traits
As BA pointed out, with convergent evolution that assumption breaks down.Silver Asiatic
June 8, 2015
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Zach
They can support that finding by comparing synonymous and non-synonymous substitutions. Guess what they found?
That they could not estimate the probability of (and therefore cannot predict) the occurrence of the non-synonymous substitutions.Silver Asiatic
June 8, 2015
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SA. Why do the synonymous mutations in Prestin make a tree that perfectly matches the mammal tree estimated from the rest of the genome?wd400
June 8, 2015
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Silver Asiatic: The main assumption is that biological similarity — even at the genetic level — is the result of inheritance from a common ancestor. Not mere similarity, but a nested pattern of traits. Silver Asiatic: then it’s clear evidence of convergent evolution. Of course, there’s no other option. They can support that finding by comparing synonymous and non-synonymous substitutions. Guess what they found?Zachriel
June 8, 2015
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wd400
a clear signal of parallel evolution
From the paper ...
What could have caused the misplacement of dolphin to the bat clade in the prestin tree? Horizontal gene transfer, DNA contamination, gene paralogy, long-branch attraction, and biased amino acid frequencies are all unlikely (see Supplemental Experimental Procedures and Figure S1A in the Supplemental Data). The only remaining reason is the convergence of the prestin sequences of echolocating bats and whales, likely resulting from a common selection for amino-acid-altering mutations that are beneficial to echolocation.
When genetic and functional similarity cannot be explained by ancestry or by any of the patchwork of exceptions above ... then it's clear evidence of convergent evolution. Of course, there's no other option. Bats and whales needed an echolocating function, so evolution selected the same kinds of mutations for them. Why do IDiots have a problem with this? I mean, there's clear evidence here. When everything else fails, it's convergent evolution, obviously. We found a gap, and evolution filled it.Silver Asiatic
June 8, 2015
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The main assumption is that biological similarity — even at the genetic level — is the result of inheritance from a common ancestor.Silver Asiatic
June 8, 2015
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Zach
Whales evolved from the same ancestor as modern artiodactyla.
Yes, mouse-deer. They were swimming for hours with widely open mouth, thus catching, like a whale, insects in the water. They then became more and more aquatic in their structure and habits, with larger and larger mouths. They gained a little weight also. Evolution made them fatter, like it did with humans.Silver Asiatic
June 8, 2015
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bornagain77 (quoting): Whenever evolutionary biologists are forced to appeal to convergent evolution, it reflects a breakdown in the main assumption, and an inability to fit the data to a treelike pattern. Convergence has been part of the theory of evolution since Darwin, so it can't "reflect a breakdown in the main assumption".Zachriel
June 8, 2015
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"The common descent of humans and other life is one of the most profound discoveries in biology," baseless Atheistic assumptions falsely parading as scientific fact are not 'profound discoveries'. They are unsubstantiated fantasies Using Numerical Simulation to Better Understand Fixation Rates, and Establishment of a New Principle - "Haldane's Ratchet" - Christopher L. Rupe and John C. Sanford - 2013 Excerpt: We then perform large-scale experiments to examine the feasibility of the ape-to-man scenario over a six million year period. We analyze neutral and beneficial fixations separately (realistic rates of deleterious mutations could not be studied in deep time due to extinction). Using realistic parameter settings we only observe a few hundred selection-induced beneficial fixations after 300,000 generations (6 million years). Even when using highly optimal parameter settings (i.e., favorable for fixation of beneficials), we only see a few thousand selection-induced fixations. This is significant because the ape-to-man scenario requires tens of millions of selective nucleotide substitutions in the human lineage. Our empirically-determined rates of beneficial fixation are in general agreement with the fixation rate estimates derived by Haldane and ReMine using their mathematical analyses. We have therefore independently demonstrated that the findings of Haldane and ReMine are for the most part correct, and that the fundamental evolutionary problem historically known as "Haldane's Dilemma" is very real. Previous analyses have focused exclusively on beneficial mutations. When deleterious mutations were included in our simulations, using a realistic ratio of beneficial to deleterious mutation rate, deleterious fixations vastly outnumbered beneficial fixations. Because of this, the net effect of mutation fixation should clearly create a ratchet-type mechanism which should cause continuous loss of information and decline in the size of the functional genome. We name this phenomenon "Haldane's Ratchet". http://media.wix.com/ugd/a704d4_47bcf08eda0e4926a44a8ac9cbfa9c20.pdfbornagain77
June 8, 2015
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Here's a figure showing bats and dolphins group together on the same tree based on Prestin sequence comparisons. http://sphotos.xx.fbcdn.net/hphotos-ash3/580955_215152708593734_182588468516825_355811_30197372_n.jpg Convergent evolution seen in hundreds of genes - Erika Check Hayden - 04 September 2013 Excerpt: “These results imply that convergent molecular evolution is much more widespread than previously recognized,” says molecular phylogeneticist Frédéric Delsuc at the The National Center for Scientific Research (CNRS) at the University of Montpellier in France, who was not involved in the study. What is more, he adds, the genes involved are not just the few, obvious ones known to be directly involved in a trait but a broader array of genes that are involved in the same regulatory networks. http://www.nature.com/news/convergent-evolution-seen-in-hundreds-of-genes-1.13679 Problem 7: Convergent Evolution Challenges Darwinism and Destroys the Logic Behind Common Ancestry - Casey Luskin February 9, 2015 Excerpt: Whenever evolutionary biologists are forced to appeal to convergent evolution, it reflects a breakdown in the main assumption, and an inability to fit the data to a treelike pattern. Examples of this abound in the literature,,,, Biochemist and Darwin-skeptic Fazale Rana reviewed the technical literature and documented over 100 reported cases of convergent genetic evolution.126 Each case shows an example where biological similarity -- even at the genetic level -- is not the result of inheritance from a common ancestor. So what does this do to the main assumption of tree-building that biological similarity implies inheritance from a common ancestor? With so many exceptions to the rule, one has to wonder if the rule itself holds merit.,,, http://www.evolutionnews.org/2015/02/problem_7_conve091161.html Newly Discovered Convergent Genetic Evolution Between Bird and Human Vocalization Poses a Severe Challenge to Common Ancestry - Casey Luskin - December 15, 2014 Excerpt: "We've known for many years that the singing behavior of birds is similar to speech in humans -- not identical, but similar -,,, "But we didn't know whether or not those features were the same because the genes were also the same." "Now scientists do know, and the answer is yes -- birds and humans use essentially the same genes to speak.",,, "there is a consistent set of just over 50 genes,,," "These changes were not found in the brains of birds that do not have vocal learning and of non-human primates that do not speak," So certain birds and humans use the same genes for vocalization -- but those genetic abilities are absent in non-human primates and birds without vocal learning? If not derived from a common ancestor, as they clearly were not, how did the genes get there? This kind of extreme convergent genetic evolution points strongly to intelligent design. http://www.evolutionnews.org/2014/12/newly_discovere092041.html Podcast: Casey Luskin on How Convergent Evolution Turns the Logic of Common Ancestry on Its Head http://www.evolutionnews.org/2015/04/listen_casey_lu_3095481.html podcast - The “Big Bang” for Birds http://www.discovery.org/multimedia/audio/2014/12/the-big-bang-for-birds/ Casey Luskin discusses the abrupt origin of birds (as well as the paper on convergent vocalization genes) on The Universe Next Door with Tom Woodward. Same Old Darwinian Drivel - June 26, 2014 Excerpt: the six electric fish lineages, all of which 'evolved' independently, used essentially the same genes and developmental and cellular pathways to make an electric organ, https://uncommondescent.com/intelligent-design/same-old-darwinian-drivel/#comment-505369bornagain77
June 8, 2015
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bornagain77: “Humans share a common ancestor with other apes.” Really???? That's the problem with ID, of course. The common descent of humans and other life is one of the most profound discoveries in biology, a foundation of everything we know about biology, yet those IDers who understand the evidence for common descent will remain silent. Do you accept that the Earth and life on Earth is billions of years old? EugeneS: It cannot account for the rise of biological function. Drift may explain the majority of molecular evolution, but adaptation requires selection.Zachriel
June 8, 2015
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http://www.cell.com/current-bi.....%2902057-0 Obviously, bats evolved from whales. And whales evolved from bears. When you go in the water and open your mouth, you eventually turn into a whale.
You want to try reading these links... The Cell paper shows the (synonymous changes only) DNA tree is identical to the expected shape, while the protein tree unites echolocators. So not only is simply untrue that bats and whales have the same genes, but the DNA sequences of the prestin gene supports the known tree of mammals, with the protein tree a clear signal of parallel evolution.wd400
June 8, 2015
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"We know that at least some molecular evolution is due to drift." It cannot account for the rise of biological function. Evolution chooses only from among existing functions. Function must exist before evolution even kicks in.EugeneS
June 8, 2015
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"Humans share a common ancestor with other apes." Really????,,, Seeing as I don't believe it is possible to change one of God's creatures into another one of God's creatures, you don't mind giving me a little demonstration of your 'strongly supported scientific fact' do you? i.e. Why do Darwinists get a free pass on ever experimentally demonstrating that Darwinism is remotely feasible?
Scant search for the Maker Excerpt: But where is the experimental evidence? None exists in the literature claiming that one species has been shown to evolve into another. Bacteria, the simplest form of independent life, are ideal for this kind of study, with generation times of 20 to 30 minutes, and populations achieved after 18 hours. But throughout 150 years of the science of bacteriology, there is no evidence that one species of bacteria has changed into another, in spite of the fact that populations have been exposed to potent chemical and physical mutagens and that, uniquely, bacteria possess extrachromosomal, transmissible plasmids. Since there is no evidence for species changes between the simplest forms of unicellular life, it is not surprising that there is no evidence for evolution from prokaryotic to eukaryotic cells, let alone throughout the whole array of higher multicellular organisms. - Alan H. Linton - emeritus professor of bacteriology, University of Bristol. http://www.timeshighereducation.co.uk/story.asp?storycode=159282
All the while, despite such poverty of evidence, Darwinists claim that generating the fantastically complex human brain by unguided material processes is beyond all doubt:
Human brain has more switches than all computers on Earth - November 2010 Excerpt: They found that the brain's complexity is beyond anything they'd imagined, almost to the point of being beyond belief, says Stephen Smith, a professor of molecular and cellular physiology and senior author of the paper describing the study: ...One synapse, by itself, is more like a microprocessor--with both memory-storage and information-processing elements--than a mere on/off switch. In fact, one synapse may contain on the order of 1,000 molecular-scale switches. A single human brain has more switches than all the computers and routers and Internet connections on Earth. http://news.cnet.com/8301-27083_3-20023112-247.html
Whatever Darwinists are doing, without any empirical basis for their claims whatsoever, whatever they are doing, it is certainly NOT science!bornagain77
June 8, 2015
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bornagain77: What makes it a ‘strongly supported scientific fact’ is “Humans evolved from ape-like ancestors. Therefore, evolution is true.” Humans share a common ancestor with other apes.Zachriel
June 8, 2015
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What makes it a 'strongly supported scientific fact' is “Humans evolved from ape-like ancestors. Therefore, evolution is true.” and What makes bats evolving from whales a 'strongly supported scientific fact' is because “Bats evolved from whale-like ancestors. Therefore, evolution is true.” please do try to keep up Zach! :)
Skull "Rewrites" Story of Human Evolution -- Again - Casey Luskin - October 22, 2013 Excerpt: "There is a big gap in the fossil record," Zollikofer told NBC News. "I would put a question mark there. Of course it would be nice to say this was the last common ancestor of Neanderthals and us, but we simply don't know." - http://www.evolutionnews.org/2013/10/skull_rewrites_078221.html “A number of hominid crania are known from sites in eastern and southern Africa in the 400- to 200-thousand-year range, but none of them looks like a close antecedent of the anatomically distinctive Homo sapiens…Even allowing for the poor record we have of our close extinct kin, Homo sapiens appears as distinctive and unprecedented…there is certainly no evidence to support the notion that we gradually became who we inherently are over an extended period, in either the physical or the intellectual sense.” Dr. Ian Tattersall: – paleoanthropologist – emeritus curator of the American Museum of Natural History – (Masters of the Planet, 2012) Whale Evolution vs. The Actual Evidence – video - fraudulent fossils revealed http://vimeo.com/30921402 Bat Evolution? - No Transitional Fossils! https://vimeo.com/127366147 "Whales, bats, horses, primates, elephants, hares, squirrels, etc., all are as distinct at their first appearance as they are now. There is not a trace of a common ancestor, much less a link with any reptile, the supposed progenitor." Harold Coffin - Zoologist - "A View Of Life"
bornagain77
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Silver Asiatic: The general argument: “Humans evolved from ape-like ancestors. Therefore, evolution is true.” Rather, it is a strongly supported scientific fact that humans share a common ancestor with other apes. From that, we have the historical context to discuss the mechanisms of that transition. Silver Asiatic: Obviously, bats evolved from whales. No. Bats and whales share a relatively distant common ancestor. Silver Asiatic: And whales evolved from bears. No. Whales evolved from the same ancestor as modern artiodactyla.Zachriel
June 8, 2015
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BA77
Zachriel, you have no evidence, and, thus, no argument to ignore. Thus, the strawman, like the evidence, only exists in your imagination.
Interesting point. When your opponent has nothing to say he can't complain about being ignored. The general argument: "Humans evolved from ape-like ancestors. Therefore, evolution is true." Now for the details of that: "Ape-like ancestors evolved from hummingbirds". Now even more details from biochemistry: "Genomic modelling shows that the presence of the same genetic structures in different organisms indicates ancestry - as in the case of whales and bats sharing the same genes for echolocation" http://www.cell.com/current-biology/abstract/S0960-9822%2809%2902057-0 Obviously, bats evolved from whales. And whales evolved from bears. When you go in the water and open your mouth, you eventually turn into a whale.Silver Asiatic
June 8, 2015
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EugeneS: That’s not the point. Of course it's the point. We know that at least some molecular evolution is due to drift. EugeneS: Genetic drift in principle is as good as random mutation in Darwin’s theory. Good for nothing, that is. Drift explains many of the patterns we observe in genomes. EugeneS: Stochastic phenomena (be it drift or random mutation) coupled with law-like necessity of selection, fixation, gravity, friction, nuclear or electromagnetic forces or whatever else, cannot adequately explain the rise of biological function. We can also show how natural selection leads to adaptation.Zachriel
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Zachriel, "The evidence indicates that different genes were involved." are they close to the 'I like coconut ice cream after dinner' gene?
John Cleese - The Scientists - 2008 https://www.youtube.com/watch?v=-M-vnmejwXo
Speaking of I like coconut ice cream genes, I hate to break this to you Zach, seeing as how infatuated with the whole gene business you are, (you must have a special I like genes gene), but the whole concept of the gene has now been overturned: In the following podcast, Dr. Sternberg’s emphasis is on ENCODE research, and how that research overturned the ‘central’ importance of the gene as a unit of inheritance. As well he reflects on how that loss of the term ‘gene’ as an accurate description in biology completely undermines the modern synthesis, (i.e. central dogma), of neo-Darwinism as a rational explanation for biology.
Podcast - Richard Sternberg PhD - On Human Origins: Is Our Genome Full of Junk DNA? Part 5 http://www.discovery.org/multimedia/audio/2014/11/on-human-origins-is-our-genome-full-of-junk-dna-pt-5/
Here are a few more references on the loss of the term gene as a ‘central’ concept in the dogma of Darwinism:
DNA at 60: Still Much to Learn – April 28, 2013 Excerpt: “Sixty years on, the very definition of ‘gene’ is hotly debated. We do not know what most of our DNA does, nor how, or to what extent it governs traits. In other words, we do not fully understand how evolution works at the molecular level.” per scientificamerican Why the ‘Gene’ Concept Holds Back Evolutionary Thinking – James Shapiro – 11/30/2012 Excerpt: The Century of the Gene. In a 1948 Scientific American article, soon-to-be Nobel Laureate George Beadle wrote: “genes are the basic units of all living things.”,,, This notion of the genome as a collection of discrete gene units prevailed when the neo-Darwinian “Modern Synthesis” emerged in the pre-DNA 1940s. Some prominent theorists even proposed that evolution could be defined simply as a change over time in the frequencies of different gene forms in a population.,,, The basic issue is that molecular genetics has made it impossible to provide a consistent, or even useful, definition of the term “gene.” In March 2009, I attended a workshop at the Santa Fe Institute entitled “Complexity of the Gene Concept.” Although we had a lot of smart people around the table, we failed as a group to agree on a clear meaning for the term. The modern concept of the genome has no basic units. It has literally become “systems all the way down.” There are piecemeal coding sequences, expression signals, splicing signals, regulatory signals, epigenetic formatting signals, and many other “DNA elements” (to use the neutral ENCODE terminology) that participate in the multiple functions involved in genome expression, replication, transmission, repair and evolution.,,, Conventional thinkers may claim that molecular data only add details to a well-established evolutionary paradigm. But the diehard defenders of orthodoxy in evolutionary biology are grievously mistaken in their stubbornness. DNA and molecular genetics have brought us to a fundamentally new conceptual understanding of genomes, how they are organized and how they function. per huffingtonpost Further Thoughts on the ENCODE/Junk DNA Debates – James Shapiro – Sept. 18, 2012 Excerpt: The ENCODE scientists have learned that it is wise to avoid interpreting the data from a fixed view of genome organization. That is why they speak of “DNA Elements” rather than genes or any other artificial categories. They tend to restrict themselves wisely to operationally defined features, such as transcription start sites (TSSs) and splice sites at exon-intron boundaries. Diogenes and like-minded people argue that we knew enough in the 1970s to understand the basic principles of genome organization. They do not accept that the flood of new information from genome sequencing and the kind of methodologies exemplified by the ENCODE project will fundamentally alter our genetic concepts. While they are certainly entitled to these opinions, I think we have to recognize that they are nothing more than that — simply opinions that fly in the face of scientific history. per huffingtonpost Landscape of transcription in human cells – Sept. 6, 2012 Excerpt: Here we report evidence that three-quarters of the human genome is capable of being transcribed, as well as observations about the range and levels of expression, localization, processing fates, regulatory regions and modifications of almost all currently annotated and thousands of previously unannotated RNAs. These observations, taken together, prompt a redefinition of the concept of a gene.,,, Isoform expression by a gene does not follow a minimalistic expression strategy, resulting in a tendency for genes to express many isoforms simultaneously, with a plateau at about 10–12 expressed isoforms per gene per cell line. Per Nature Time to Redefine the Concept of a Gene? – Sept. 10, 2012 Excerpt: As detailed in my second post on alternative splicing, there is one human gene that codes for 576 different proteins, and there is one fruit fly gene that codes for 38,016 different proteins! While the fact that a single gene can code for so many proteins is truly astounding, we didn’t really know how prevalent alternative splicing is. Are there only a few genes that participate in it, or do most genes engage in it? The ENCODE data presented in reference 2 indicates that at least 75% of all genes participate in alternative splicing. They also indicate that the number of different proteins each gene makes varies significantly, with most genes producing somewhere between 2 and 25. Based on these results, it seems clear that the RNA transcripts are the real carriers of genetic information. This is why some members of the ENCODE team are arguing that an RNA transcript, not a gene, should be considered the fundamental unit of inheritance. http://networkedblogs.com/BYdo8 Duality in the human genome – Nov. 28, 2014 Excerpt: The gene, as we imagined it, exists only in exceptional cases. “We need to fundamentally rethink the view of genes that every schoolchild has learned since Gregor Mendel’s time. Moreover, the conventional view of individual mutations is no longer adequate. Instead, we have to consider the two gene forms and their combination of variants,”,,, “Our investigations at the protein level have shown that 96 percent of all genes have at least 5 to 20 different protein forms.,,, per MedicalXpress Information killed the Central Dogma too – April 10, 2014 Abstract: The classical view of information flow within a cell, encoded by the famous central dogma of molecular biology, states that the instructions for producing amino acid chains are read from specific segments of DNA, just as computer instructions are read from a tape, transcribed to informationally equivalent RNA molecules, and finally executed by the cellular machinery responsible for synthesizing proteins. While this has always been an oversimplified model that did not account for a multitude of other processes occurring inside the cell, its limitations are today more dramatically apparent than ever. Ironically, in the same years in which researchers accomplished the unprecedented feat of decoding the complete genomes of higher-level organisms, it has become clear that the information stored in DNA is only a small portion of the total, and that the overall picture is much more complex than the one outlined by the dogma. The cell is, at its core, an information processing machine based on molecular technology, but the variety of types of information it handles, the ways in which they are represented, and the mechanisms that operate on them go far beyond the simple model provided by the dogma. per UncommonDecent “Physiology Is Rocking the Foundations of Evolutionary Biology”: Another Peer-Reviewed Paper Takes Aim at Neo-Darwinism – Casey Luskin March 31, 2015 Excerpt: Noble doesn’t mince words: “It is not only the standard 20th century views of molecular genetics that are in question. Evolutionary theory itself is already in a state of flux (Jablonka & Lamb, 2005; Noble, 2006, 2011; Beurton et al. 2008; Pigliucci & Muller, 2010; Gissis & Jablonka, 2011; Shapiro, 2011). In this article, I will show that all the central assumptions of the Modern Synthesis (often also called Neo-Darwinism) have been disproved.” Noble then recounts those assumptions: (1) that “genetic change is random,” (2) that “genetic change is gradual,” (3) that “following genetic change, natural selection leads to particular gene variants (alleles) increasing in frequency within the population,” and (4) that “inheritance of acquired characteristics is impossible.” He then cites examples that refute each of those assumptions,,, He then proposes a new and radical model of biology called the “Integrative Synthesis,” where genes don’t run the show and all parts of an organism — the genome, the cell, the body plan, everything — is integrated. http://www.evolutionnews.org/2015/03/physiology_is_r094821.html
bornagain77
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