New genes born by accident lead to evolutionary innovation

December 31, 2015
genes
This image shows the coding region in a segment of eukaryotic DNA. Credit: National Human Genome Research Institute

Novel genes are continuously emerging during evolution, but what drives this process? A new study, published in PLOS Genetics, has found that the fortuitous appearance of certain combinations of elements in the genome can lead to the generation of new genes. This work was led by Jorge Ruiz-Orera and Mar Albà from Hospital del Mar Medical Research Institute in Barcelona (IMIM-ICREA).

In every , there are sets of genes, which are unique to that particular species. In this study, the scientists first identified thousands of genes that were specific to human or chimpanzee. Then, they searched the macaque genome and discovered that this species had significantly less element motifs in the corresponding genomic sequences. These motifs are recognized by proteins that activate gene expression, a necessary step in the formation of a new gene.

The formation of genes de novo from previously non-active parts of the genome was, until recently, considered highly improbable. This study has shown that the mutations that occur normally in our genetic material may be sufficient to explain how this happens. Once expressed, the can act as a substrate for the evolution of new molecular functions. This study identified several candidate human proteins that bear no resemblance to any other known protein. What they do is an enigma still to be resolved.

Explore further: Parts of genome without a known function may play a key role in the birth of new proteins

More information: Ruiz-Orera J, Hernandez-Rodriguez J, Chiva C, Sabidó E, Kondova I, Bontrop R, et al. (2015) Origins of De Novo Genes in Human and Chimpanzee. PLoS Genet 11(12): e1005721. DOI: 10.1371/journal.pgen.1005721

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BartV
2.3 / 5 (15) Jan 01, 2016
Novel genes are continuously emerging during evolution....


What? A "science" article starts with a statement that has never been observed, let alone replicated. If evolution rests its foundation merely on man's whims and imagination, then it is truly fit for the garbage can.

The rest of the article is meaningless.

Torbjorn_Larsson_OM
5 / 5 (13) Jan 01, 2016
What? A "religious" comment starts with a magic idea that has never been observed, let alone replicated. If religion rests its foundation merely on man's whims and imagination, then it is truly fit for the garbage can.

Trolling established science is meaningless:

"Here, I review the origin and evolution of new genes and their functions in eukaryotes, an area of research that has made rapid progress in the past decade thanks to the genomics revolution. Indeed, recent work has provided initial whole-genome views of the different types of new genes for a large number of different organisms."

[ http://genome.csh...ull.html ]

That review was from 2010. With 5 more years, the observed ways (and genes) would be a much larger subject.

If you don't know science, either ask or ... open your mouth in other ways and reveal what an ignorant buffoon you are.
viko_mx
2.4 / 5 (14) Jan 01, 2016
"Novel genes are continuously emerging during evolution, but what drives this process?""

This is not true. New genes can not emerge during fictional evolution without the programmer who to ensure their functional compatibility with the existing genetic information and to implement in addition new controlling mechanisms for this new compatible information. The programing of complex systems is not easy task. I now it from my personal experience. Random events do not work.

Question:

If the probability random mutations to cause lost of genetic information and functionality is many times greater than the probability to cause the emergence of new useful information which is fully compatible with the existing old genetic information (in the reality probability is zero - "0"), can we expect billion of years of evolution?
matt_s
2.8 / 5 (13) Jan 02, 2016
" New genes can not emerge during fictional evolution without the programmer who to ensure their functional compatibility with the existing genetic information and to implement in addition new controlling mechanisms for this new compatible information."

Proof? Evidence? Lots of unbased assumptions on your part.

If the probability random mutations to cause lost of genetic information and functionality is many times greater than the probability to cause the emergence of new useful information which is fully compatible with the existing old genetic information (in the reality probability is zero - "0")

Proof? Evidence? More unbased assumptions.

Torbjorn_Larsson_OM
5 / 5 (7) Jan 02, 2016
"New genes can't emerge".

I can just C&P:

Trolling established science is meaningless:

"Here, I review the origin and evolution of new genes and their functions in eukaryotes, an area of research that has made rapid progress in the past decade thanks to the genomics revolution. Indeed, recent work has provided initial whole-genome views of the different types of new genes for a large number of different organisms."

[ http://genome.csh...ull.html ]

That review was from 2010. With 5 more years, the observed ways (and genes) would be a much larger subject.

If you don't know science, either ask or ... open your mouth in other ways and reveal what an ignorant buffoon you are. So you did ask, but your question is meaningless as it is based on an erroneous claim. The question you should ask is how genes change the triplet code to achieve function. (Information content is an unnecessary measure to study.) The answer is by selection.
Torbjorn_Larsson_OM
5 / 5 (8) Jan 02, 2016
[ctd] Now, mind that the process happens over a population and generations, so you need to understand how selection works there if you want to tease out more detail. That is the area of population genetics, which again study sequence changes and not information changes since it is irrelevant.

FWIW, biologists understand and have verified information changes in the genome by using Shannon information and Kolmogorov complexity measures because it is something you can check even if it isn't helpful to understand how the biology works, so there are some papers on that.

The information is acquired, trough selection, in the same way that everyone learns. That is, the genome learn from the environment what alleles (functions) that worked in the previous generation (but the environment changes slow enough). The learning mechanism is bayesian learning on positive and negative fitness, i,e, selection on a population.

Torbjorn_Larsson_OM
5 / 5 (7) Jan 02, 2016
[ctd] In short, evolution doesn't need to know anything obviously, because it started out with simple random replicating strands. Those strands varied randomly, so had maximized their Kolmogorov complexity - their information content.

What selection dies is whittle away genome information to replace it with a less dense information structure of regularities - mirroring the regularities of the environment. These somewhat more regular genes are recipe information, channeled from the environment as Shannon information.

That is either you consider the modern genome to contain less information - less randomness - or more useful information - more regularities. In either case all the information comes from the environment (nature).
Torbjorn_Larsson_OM
5 / 5 (7) Jan 02, 2016
[ctd] If you ask about the information content of the structure formation in the universe (cosmology), it is the same. The inflation field spawned quantum fluctuations that - after caustics formation and gravity assembly - makes up the random cosmological filaments that spawned galaxies. The information content of randomness decreases locally as the useful regularities increases due to physical processes.

The information content globally increases as entropy increases. That is another well understood physical process. The universe started out simple, then it grew complexity thanks to physics, in the future everything will dilute to simplicity once again. Drivers are entropy and cosmology, simple physical processes that happen to produce less useful (random) and useful (regularities) information, because it is a characteristic of what they do.
Torbjorn_Larsson_OM
5 / 5 (7) Jan 02, 2016
I should add that to ask where recipe (or programming) information comes from is rather uninformed, especially if one is a programmer. No one knew that eggs could be eaten before they tried (and likely failed on rotten eggs), no one knew they could be fried, et cetera.

Similarly all the programs we can put in a computer were never envisioned or put in the memory of the first computer, programming was painfully learned from the interaction between the computer CPU/memory and its environment (I/O, programmer, program use).

The programmer (and his or her customer) is hence just a dumb trial and learning device, the full set or programmers (and their customers) are equivalent to the biological variation and selection processes both. Programmers can be replaced by more capable programs that themselves develop software by the same methods, and that automation is a good analogy to what biology has done for 4 billion years because chemistry allowed it and thermodynamics drove it.
Torbjorn_Larsson_OM
5 / 5 (7) Jan 02, 2016
Errata: "In short, evolution doesn't need to know anything obviously..."

In short, evolution doesn't need to know anything obviously, because it started out with simple random replicating strands. Those strands varied randomly, so had maximized their Kolmogorov complexity - their information content.

What selection does is whittle away genome information to replace it with a less dense information structure of regularities ... [et cetera. Then:] In short, evolution doesn't need to know anything initially, it simply needs to be able to learn. That ability is an ability that a population of genomes (organisms) have by the natural mechanisms of variation and selection.
viko_mx
3.5 / 5 (8) Jan 04, 2016
@matt_s

Your spammers tacticс does not make sense. Do you need to prove you that salt is salty or the water is wet?

I'm not going to convince those who have refused to think because of their passions. I can not help them.
I want to draw attention to honest and thinking people on the scientific facts.
viko_mx
3.2 / 5 (9) Jan 04, 2016
Random variations obey the established during the creation event of the universe physical laws. They do not change these laws, physical constants and fundamental forces, to be capable to increase the order (information) in the system.

The random change in the "replicating strands" - common meaningless concept, produce only useless noise. In fact chemical reactions obey certain law. There is now lawlessness in nature except human lawlessness because of pride, vanity and stupidity.

Scientist are unable to make proteins in laboratory conditions without the help of living organisms. Nor DNA. If this task were easy, it would not out there in all living organisms such complexes precisely synchronized and energetically provided mechanisms for this despite a high optimization of the biological processes in them.

The universe exist because of life. If there are not intelligent beings who control it and to who this physical environment to serve, it existence is meaningless.
viko_mx
3.5 / 5 (8) Jan 04, 2016
To be possible evolution, random mutations must produce more positive than negative effects on the living organisms. But such thing directly contradict the physical reality. Ironically, it does not known to the scientific community even a single positive mutation. Аging of all material objects in the universe is a manifestation of one way entropy and loss of information due to entropic processes. Entropy can be withstand only by the ideas, the will and the actions of intelligent beings within certain limits.
viko_mx
3.2 / 5 (9) Jan 04, 2016
And only the Creator can control it 100 % because is outside of the system and the primary cause of everything.
Mike_Massen
2.1 / 5 (11) Jan 04, 2016
viko_mx claims
And only the Creator can control it 100 % because is outside of the system and the primary cause of everything.
But can't tell us anything about his claimed creator - why is that - why is it so Very silent ?

viko_mx you have been told before and Never been able to refute it, that the universe has immense self-organisational properties.

Eg. Have you noticed snowflakes have more 'information' re regular structure than mere gaseous water vapour - this is Clear Evidence against your claims elsehwere that there can only be disorder ?

And what about crystals viko_mx ?

What about bonding discontinuities leading to formamide, then Guanine etc All these patterns are built in - there is NO need for any (personal) creator to talk to only one man at a time, all gods are mere claim, nothing definitive, no feedback, only ideas, some sincere to hold society together with self-evident laws based on empathy - shared with Animals including Bonobo Apes :P

thefurlong
5 / 5 (4) Jan 04, 2016
@Mike_Massen
viko_mx doesn't like to respond to arguments he does not have the competence to answer. This allows him to keep deluding himself while never having to learn a thing.

Several of us have pointed out snowflake and crystal formation, and other physical processes in which order arises from disorder. I have also explained to him that order is not the same as information, and that, with constraints, some forms of order can be synonymous with a LACK of information.

He never responds.
Torbjorn_Larsson_OM
5 / 5 (4) Jan 04, 2016
@viko: I see you now accept that new genes are observed to occur by entirely natural processes.

"The random change in the "replicating strands" - common meaningless concept".

That mechanism is one of the observations in the linked paper.

"Scientist are unable to make proteins in laboratory conditions without the help of living organisms. Nor DNA."

Both peptides and nucleic acid is made all over the universe, from the atmosphere of carbon stars on. [ http://www.dailyg...se-.html ]

Now on to your magic ideas that makes claims on science:

"Random variations obey the established during the creation event of the universe physical laws."

What event? For all we know inflation can be backwards eternal as much as our universe is forwards eternal. Remember, extraordinary claims need extraordinary evidence.

[tbctd]
Torbjorn_Larsson_OM
5 / 5 (4) Jan 04, 2016
[ctd]

ADDED: Re random change in the "replicating strands", that is also why you isn't an exact clone of one of your parents. Have you never thought about why you aren't!?

But even if quantum fluctuations once didn't exist and now does, so what? They are still unordered, of maximum information, and doesn't represent any structured information. I went through how structure appears in cosmology and from there (from habitable planets) biology.

This is all well understood, the question is rather if you can be bothered to start study population genetics where the science at hand lies.

The rest of your comment is just your magic incantations, full of fury, signifying nothing, all nonsense according to modern science. Lay off the magic claims and incantations, if you have a question about science that we can help you with.

Who knows, maybe you can start read for understanding, as they say: "rare events do happen"!
Mike_Massen
2.2 / 5 (10) Jan 04, 2016
Thanks to thefurlong who offered
I have also explained to him that order is not the same as information, and that, with constraints, some forms of order can be synonymous with a LACK of information
Indeed, hence my adding quotes over the 'information', like so many viko_mx's ability in inference, deduction & basic logic is lacking :-(

thefurlong observed
He never responds
Well never with anything convergent on essential truths, if & when he does its so often bland proselytizing, which in way is an example of why those like him have no credibility and continues to lose credibility as the competition of "Claim vs Evidence" continues which supports the rationality against arbitrary emotional attachments...

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