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Human evolution: Well, this IS a new take on “genetically modified organisms” (GMOs)

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From the Economist:

Alastair Crisp and Chiara Boschetti of Cambridge University, and their colleagues, have been investigating the matter. Their results, just published in Genome Biology, suggest human beings have at least 145 genes picked up from other species by their forebears. Admittedly, that is less than 1% of the 20,000 or so humans have in total. But it might surprise many people that they are even to a small degree part bacterium, part fungus and part alga.

Dr Crisp and Dr Boschetti came to this conclusion by looking at the ever-growing public databases of genetic information now available. They did not study humans alone. They looked at nine other primate species, and also 12 types of fruit fly and four nematode worms. Flies and worms are among geneticists’ favourite animals, so lots of data have been collected on them. The results from all three groups suggest natural transgenics is ubiquitous.

It’s called horizontal gene transfer, and we have been covering it for years.

After all, it is a form of evolution for which there is lots of evidence, unlike the Darwin-in-the-schools textbook rot.

It is nice to be able to talk about evolution when there is actually a subject other than the impostures of the Darwin lobby. We hope to do much more on this in the future.

See also: Human evolution as a narrative

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Comments
Piotr, I am convinced that this is a plausible mechanism for potential transfer of genetic information and have read of it before. HOwever what I would be interested in knowing is, are there any known concensous insertion sequences typical of such an event, or ways to strongly support a gene was inserted by the phage rather than already present? Without assuming it must be inserted because it appears t of sequence with phylogeny? I.e. does the insertion by phage leave a measurable signature that isn't usually present in the host? A type of promoter site or similar unique to the phage?Dr JDD
March 26, 2015
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What are the mechanisms of HGT? I mean, how likely is it for a gene to be transferred from one animal to another, make its way to sperm or egg and finally result in an offspring with the newly acquired gene? Inquiring minds and all that.Mapou
March 26, 2015
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#23 Aurelio Smith,
I’d like to see a convincing suggestion of how a gene could transfer horizontally and get into the gamete that becomes egg or sperm for the next generation.
What about intracellular "reproductive parasites" specialising in infecting ovaries and mature eggs to make sure they are passed to their host's offspring? The parasite may undergo "domestication" until it becomes an endosymbiont useful for the host -- for example producing some enzymes by way of paying the rent. Wolbachia is one such case, and it's a notorious source of (phage-mediated) horizontally transferred stuff in many arthropods and nematodes (including the insertion of its nearly complete genome into the DNA of one Drosophila species). http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3068000/ [Edited to add: http://www.sciencemag.org/content/317/5845/1753 ] Looks quite convincing to me.Piotr
March 26, 2015
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Cupcake, you must be lost, as usual-
Microbial infections are the likeliest kind of contact that can lead to horizontal transfer. HGT is known to have happened in eukaryotes (including primates), so it must be possible, though infrequent.- Piotr 22
Joe
March 26, 2015
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Targeting the germline?
It is a POSSIBILITY, Piotr. Unlike unguided evolution which isn't even feasible.Joe
March 26, 2015
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Mark Frank:
After all it has nothing much to do with ID.
Horizontal gene transfer has everything to do with intelligent design. HGT is analogous to what software engineers call multiple inheritance. It is a well-known design technique. HGT destroys the strictly nested hierarchy of Darwinists that one would expect from common descent. But wouldn't you know it? HGT is now part and parcel of Darwinian evolution. Of course.Mapou
March 26, 2015
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Any contact has the possibility of transferring biological material.
Targeting the germline? (otherwise it will not become heritable). "Any contact" can't be enough, or your genome would be contaminated with banana DNA from eating bananas. Microbial infections are the likeliest kind of contact that can lead to horizontal transfer. HGT is known to have happened in eukaryotes (including primates), so it must be possible, though infrequent. The question is how infrequent. It isn't true that the article claims "human beings" have picked up 145 genes from other species. As far as I can see, according to the authors only one (1) of them has been picked up by the human lineage since the human/chimp split, and the majority are "ancient" in the sense that the transfer took place anywhere between the origin of Chordata (about 520 Mya) and the common ancestor or Primates (about 65 Mya). That's about 100 transfers in more than 400 My -- one such event per four million years, on an average.Piotr
March 26, 2015
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It would be 99.99% of fossils support UCD, so it's very probable this this one fossil was not really laid down in the Cambrian. That's just how probability works. If you could actually prove the fossil was Cambrian then there would be a big problem from UCD, but you'd need lots of evidene to do so.
Since when in science do we need a certain percentage of evidence to falsify a theory?
Are you serious? Does ID go so far as to to doubt probability now?
One apple falling the wrong way from a tree could falsify the theory of gravity despite the billions falling the “right” way.
What would the wrong way be?
So if it is fine with the 99.5% of “vertically” transferred genes what’s the big deal?
You'll have to ask News, I guess.wd400
March 26, 2015
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By the way wd400 I would agree with you that HGT does not pose any problems to evolutionary theory or UCD, in my personal opinion. The problem I have is assuming that something that doesn't fit with expectations of the tree of life and UCD must be HGT. That to me is bad science, and like you say it may not even be HGT but could be gene loss or other similar mechanisms that explain this. My points are to highlight the mentality of people in this field. It is a feature of many aspects of published work.Dr JDD
March 26, 2015
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wd400: So if a rabbit fossil was found in a strata that predated say the Cambrian era that apparently as touted sneeringly by many materialists is an example of something that would falsify UCD etc. That is, 1 fossil. So would the argument be "but 99.99%of fossils fit the evolutionary UCD so this 1 fossil isn't a problem"?? My question remains, how do we know it is HGT? Since when in science do we need a certain percentage of evidence to falsify a theory? One apple falling the wrong way from a tree could falsify the theory of gravity despite the billions falling the "right" way. And again, ID and rejecting UCD is perfectly in line with what is observed with homology between species that does not simply align to common descent but also common design with some limited common descent, for example. So if it is fine with the 99.5% of "vertically" transferred genes what's the big deal?Dr JDD
March 26, 2015
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This is perhaps an example of how things are not falsifiable in the evolutionary paradigm. If you ask the question, “what would falsify common descent” one piece of evidence would surely be finding genes in distantly related species that were not present in more recently related species. There may be other explanations eg. HGT but you cannot assume that unless you are determined that you are not even going to entertain that the tree of life may be wrong.
"finding genes in distantly related species that were not present in more recently related species" requires only gene loss in some lineages (ineed, the limiting taxonomic sampling in this paper is one reason to be suspicious of these results). More generally, it's not a case of not "entertaining that the tree of life may be wrong" (which I guess means there is no tree?). It's the fact common descent is so well supported by so much evidence. The prior that tree of life is "right" is so large that you will require a lot more than 100 genes that might have taken another route through time to change it very much.wd400
March 26, 2015
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Tjguy - was typing my response I guess as you were too - seems as though we are on the same track of thinking. This was the point of my first post yet smiddyone failed to contemplate that which proves the point of the limited scope of addressing evidence for potential multiple hypotheses. We couldn't possibly falsify the tree of life and UCD therefore it MUST be something else. THe very fact something is not falsifiable makes it religious faith, not science. The very thing theists are accused of. By the way, I am not opposed to this being HGT nor am I saying it is not. I would like to know though how we can be certain it is HGT other than fitting in the paradigm of UCD and the ToL currently accepted and I would also like people to do science properly and understand all theories are falsifiable and you should always consider alternative hypotheses that fit the data.Dr JDD
March 26, 2015
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I guess it's time for the customary question: Why do you think HGT is a problem for mainstream evolutionary biology? This quote is particularly wierd:
After all, it is a form of evolution for which there is lots of evidence, unlike the Darwin-in-the-schools textbook rot.
Even you accept this study on face value you end up with ~99.5% of protein coding genes in humans having only verticle inheritance for the 600 million years or so. Part of the overwhelming evidence for common descent which, indeed, is taught in schools. On the other hand, this single paper says it possiblethat ~0.5% of those protein coding genes came into our ancestors horizontally, before being passed on vertically. In fact, they don't really do enough to rule out other scenarios that could explain their results, so it's not clear if even that half a percent came from prokaryotes. So, we have overwhelming evidence that the overwhelming majority of the genome has been passed on vertically. And some evidence that tiny fraction moved into our genome horizontally. And you want to sneer at the people teaching the overwhelming evidence for the overwhelming majority?wd400
March 26, 2015
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Smiddyone, thank you for demonstrating the 1-dimensional nature of the typical materialist thinking. The a priori assumption is that if a gene is present in an organism but not in what is determined to be a recent predecessor of that organism but in something much more distant - then it must be HGT. Unless of course there are very specific insertion sequences that suggest transmission via phage or something else known (or thought) to be a vehicle for HGT and thus a way to verify that these were indeed inserted, you are working on the assumption it was HGT due to phylogenetic trees. This is perhaps an example of how things are not falsifiable in the evolutionary paradigm. If you ask the question, "what would falsify common descent" one piece of evidence would surely be finding genes in distantly related species that were not present in more recently related species. There may be other explanations eg. HGT but you cannot assume that unless you are determined that you are not even going to entertain that the tree of life may be wrong. So smiddyone seeing as you seem to know so much about HGT please can you tell me how the researchers here determined this was HGT specifically other than the assumption that it must be given these organisms sit so distant on the tree of life? I am actually genuinely interested to know.Dr JDD
March 26, 2015
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Has anyone read Casey Luskin's article about HGT here? http://www.evolutionnews.org/2015/03/a_big_problem_f094701.html It was very enlightening for me! It seems like it is another example of "Heads I win, tails you lose" type of argument. When the same genes exist in supposed predecessors, it is evidence of common descent and then when there are totally different genes, instead of evidence against common descent, it is said to be evidence of HGT and therefore evidence of common descent! It is just another example of how contradictory data is finagled to provide "evidence" for common descent. They find a way to tweak the paradigm to make it work, but like Dr JDD asked
how do we know that these genes have undergone HGT? Are there any viable alternative hypotheses that could fit seeing genes in humans and other organisms that do not fit on a standard phylogenetic tree?
Smiddyone gives the following non-answer:
suggest human beings have at least 145 genes picked up from other species by their forebears. Where else would they come from?
Well, thinking within the Materialist paradigm, I guess there is no other answer. Their options are limited. So sure, just jump on the bandwagon and claim it as evidence for HGT and therefore unguided unintelligent evolution. But is it really? Just sayin' so doesn't make it so in real science. Maybe the data doesn't really support common descent as well as we have been told!tjguy
March 26, 2015
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"Common Ancestor" term needs to be retired. "Common Predecessors", plural, matches up with the evidence so much better. C'mon, ancestors can be dead but NOT extinct.ppolish
March 26, 2015
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Have the authors really demonstrated such widespread HGT in primates?
Why are you so surprised? Any contact has the possibility of transferring biological material.Joe
March 26, 2015
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Mark Frank:
Darwin-in-the-schools account of how evolution happens comprises two elements – unguided variation and natural selection.
Both of which have proven to be impotent. Did you have a point?
After all it has nothing much to do with ID.
It has nothing to do with unguided evolution.Joe
March 26, 2015
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#9 DNA_Jock
who here actually finds the Crisp et al. paper credible?
13 pages of technical material is a bit much for me. I will wait for the scientific community to respond.Mark Frank
March 26, 2015
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Could we have a quick informal poll: who here actually finds the Crisp et al. paper credible? Have the authors really demonstrated such widespread HGT in primates?DNA_Jock
March 26, 2015
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It’s called horizontal gene transfer, and we have been covering it for years.
Not, I think, as long as the scientific community.
After all, it is a form of evolution for which there is lots of evidence, unlike the Darwin-in-the-schools textbook rot.
Darwin-in-the-schools account of how evolution happens comprises two elements - unguided variation and natural selection. The natural selection bit applies equally to genes acquired horizontally or vertically. There is far more evidence for vertical transfer of genes then for horizontal transfer (or you trying to say there is no evidence for meiosis and mitosis?). Growing evidence for some horizontal gene transfer at the multicellular level is interesting and introduces another form of unguided variation which I guess will eventually find its way into textbooks (maybe has already?)
It is nice to be able to talk about evolution when there is actually a subject other than the impostures of the Darwin lobby. We hope to do much more on this in the future.
Or you could simply read the literature. After all it has nothing much to do with ID.Mark Frank
March 26, 2015
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Box, it's all Common Descent and unguided evolution. :roll:Joe
March 26, 2015
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suggest human beings have at least 145 genes picked up from other species by their forebears.
OK so you are saying it supports limited common descent as in humans are descendants of other humans.Joe
March 26, 2015
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Everything seems to confirm common descent these days.Box
March 26, 2015
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suggest human beings have at least 145 genes picked up from other species by their forebears. Where else would they come from?smiddyone
March 26, 2015
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How does HGT confirm common descent? Please be specificJoe
March 26, 2015
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It’s called horizontal gene transfer, and we have been covering it for years. Which confirms common descentsmiddyone
March 26, 2015
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So how do we know that these genes have undergone HGT? Are there any viable alternative hypotheses that could fit seeing genes in humans and other organisms that do not fit on a standard phylogenetic tree?Dr JDD
March 26, 2015
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